This report has goseq results for BMI when:

  1. Genes with FDR < 0.1 marked as DE
  2. Genes from above list with positive effect marked as differentially expressed
  3. Genes from above list with negative effect marked as differentially expressed

This report was generated on June 18 2015

Goseq results also saved in csv files located on snowwhite in directory: /net/snowwhite/home/beckandy/tissue/datafreeze4/goseq/jun3/12junReps/FDR/csv

Step 1: Load in all the necessary data/libraries

library(goseq)

## Loading required package: BiasedUrn
## Loading required package: geneLenDataBase
## Loading required package: DBI

library(qvalue)

fName <- "/net/snowwhite/home/beckandy/tissue/datafreeze4/goseq/traits/peer_k03_bmi_all_genes.txt"
outFile <- "bmi"

data <- read.table(fName, as.is=T, header=T)

gene_length_file <- "/net/snowwhite/home/beckandy/tissue/datafreeze4/goseq/jun3/length.composite.gene.models.gencode.v19"
gene_lengths = read.table(gene_length_file, header=T, as.is=T);
gene_lengths$gene = sapply(gene_lengths$gene, function(x){ unlist(strsplit(x, split="[.]"))[1] });

data$gene <- sapply(data$gene, function(x){ unlist(strsplit(x, split="[.]"))[1] });

data <- merge(data, gene_lengths, by="gene", all.x=T)
data <- data[order(data$p.value),]
data$q.value <- qvalue(data$p.value)$qvalues
data$rank <- seq(1,length(data[,1]))

minRow <- 20

Step 2: Create genes vectors

The first vector simply marks the top 1000 genes as differentially expressed. The second and third vectors mark the genes with positive or negative effect in the top 1000 as differentially expressed.

genes <- as.numeric(data$q.value <= 0.1)
genesPos <- as.numeric(data$q.value <= 0.1 & data$effect > 0)
genesNeg <- as.numeric(data$q.value <= 0.1 & data$effect < 0)

names(genes) <- data$gene
names(genesPos) <- data$gene
names(genesNeg) <- data$gene

There are 3665 DE genes with postive effect and 3020 DE genes with negative effect.

Step 3: PWFs

pwf <- nullp(genes,"hg19","ensGene",bias.data=data$length, plot.fit=FALSE)

pwfPos=nullp(genesPos,"hg19","ensGene",bias.data=data$length, plot.fit=FALSE)

pwfNeg=nullp(genesNeg,"hg19","ensGene",bias.data=data$length, plot.fit=FALSE)

Step 4: run goseq

go <- goseq(pwf,"hg19","ensGene",test.cats=c("GO:BP"))
goPos <- goseq(pwfPos,"hg19","ensGene",test.cats=c("GO:BP"))
goNeg <- goseq(pwfNeg,"hg19","ensGene",test.cats=c("GO:BP"))

rownames(go) <- NULL
rownames(goPos) <- NULL
rownames(goNeg) <- NULL

# Fix problem with some p-values being slightly more than 1
go$over_represented_pvalue[go$over_represented_pvalue>1]=1;
go$under_represented_pvalue[go$under_represented_pvalue>1]=1;
goPos$over_represented_pvalue[goPos$over_represented_pvalue>1]=1;
goPos$under_represented_pvalue[goPos$under_represented_pvalue>1]=1;
goNeg$over_represented_pvalue[goNeg$over_represented_pvalue>1]=1;
goNeg$under_represented_pvalue[goNeg$under_represented_pvalue>1]=1;

go$q.value <- qvalue(go$over_represented_pvalue)$qvalues
goPos$q.value=qvalue(goPos$over_represented_pvalue)$qvalues
goNeg$q.value=qvalue(goNeg$over_represented_pvalue)$qvalues

go$q.value2 <- qvalue(go$under_represented_pvalue)$qvalues
goPos$q.value2=qvalue(goPos$under_represented_pvalue)$qvalues
goNeg$q.value2=qvalue(goNeg$under_represented_pvalue)$qvalues

Top 1000 Results

Over enriched categories (62)

rowN <- max(minRow, sum(go$q.value<=0.05))
cat(kable(go[1:rowN,c("category","term","numInCat","numDEInCat","q.value")],format="html"));
category term numInCat numDEInCat q.value
GO:0006414 translational elongation 121 100 0.0000000
GO:0006415 translational termination 95 83 0.0000000
GO:0000184 nuclear-transcribed mRNA catabolic process, nonsense-mediated decay 118 97 0.0000000
GO:0006413 translational initiation 167 121 0.0000000
GO:0006614 SRP-dependent cotranslational protein targeting to membrane 107 86 0.0000000
GO:0006613 cotranslational protein targeting to membrane 109 87 0.0000000
GO:0072599 establishment of protein localization to endoplasmic reticulum 111 88 0.0000000
GO:0045047 protein targeting to ER 110 87 0.0000000
GO:0070972 protein localization to endoplasmic reticulum 128 96 0.0000000
GO:0006612 protein targeting to membrane 171 116 0.0000000
GO:0000956 nuclear-transcribed mRNA catabolic process 184 121 0.0000000
GO:0006412 translation 496 260 0.0000000
GO:0019083 viral transcription 158 105 0.0000000
GO:0043624 cellular protein complex disassembly 174 113 0.0000000
GO:0043241 protein complex disassembly 195 122 0.0000000
GO:0019080 viral gene expression 168 108 0.0000000
GO:0006402 mRNA catabolic process 196 122 0.0000000
GO:0044033 multi-organism metabolic process 178 110 0.0000000
GO:0090150 establishment of protein localization to membrane 296 165 0.0000000
GO:0032984 macromolecular complex disassembly 205 123 0.0000000
GO:0006401 RNA catabolic process 222 128 0.0000000
GO:1902578 single-organism localization 426 214 0.0000000
GO:1902580 single-organism cellular localization 426 214 0.0000000
GO:0072657 protein localization to membrane 371 190 0.0000000
GO:0061024 membrane organization 778 357 0.0000000
GO:0006886 intracellular protein transport 758 346 0.0000000
GO:0044802 single-organism membrane organization 638 297 0.0000000
GO:0072594 establishment of protein localization to organelle 456 222 0.0000001
GO:0006605 protein targeting 497 239 0.0000001
GO:0071822 protein complex subunit organization 1283 547 0.0000001
GO:0070727 cellular macromolecule localization 1129 489 0.0000001
GO:0043933 macromolecular complex subunit organization 1450 609 0.0000002
GO:0034613 cellular protein localization 1124 486 0.0000002
GO:0033365 protein localization to organelle 603 280 0.0000002
GO:0016482 cytoplasmic transport 825 368 0.0000002
GO:1902582 single-organism intracellular transport 1181 505 0.0000003
GO:0015031 protein transport 1320 557 0.0000005
GO:0044267 cellular protein metabolic process 3491 1360 0.0000012
GO:0044403 symbiosis, encompassing mutualism through parasitism 727 323 0.0000017
GO:0044419 interspecies interaction between organisms 727 323 0.0000017
GO:0008104 protein localization 1760 718 0.0000028
GO:0045184 establishment of protein localization 1422 590 0.0000030
GO:0033036 macromolecule localization 2032 815 0.0000090
GO:0046907 intracellular transport 1406 579 0.0000134
GO:0016032 viral process 674 297 0.0000166
GO:0044764 multi-organism cellular process 682 300 0.0000175
GO:0019058 viral life cycle 303 147 0.0000214
GO:0016071 mRNA metabolic process 615 273 0.0000265
GO:0019538 protein metabolic process 4128 1571 0.0000265
GO:0051641 cellular localization 2267 895 0.0000316
GO:0006417 regulation of translation 249 126 0.0000357
GO:0022411 cellular component disassembly 412 190 0.0001104
GO:0071702 organic substance transport 1993 788 0.0003628
GO:0044265 cellular macromolecule catabolic process 798 338 0.0008804
GO:0051649 establishment of localization in cell 1974 776 0.0013786
GO:0009057 macromolecule catabolic process 983 405 0.0036545
GO:0044237 cellular metabolic process 8652 3131 0.0168734
GO:0065003 macromolecular complex assembly 1091 437 0.0244481
GO:0044260 cellular macromolecule metabolic process 6484 2374 0.0250056
GO:0055114 oxidation-reduction process 896 361 0.0267569
GO:0006901 vesicle coating 38 25 0.0303621
GO:0010608 posttranscriptional regulation of gene expression 422 183 0.0419838

Under enriched (0)

go <- go[order(go$under_represented_pvalue),]
rowN <- max(minRow, sum(go$q.value2<=0.05))
cat(kable(go[1:rowN,c("category","term","numInCat","numDEInCat","q.value2")],format="html"));
category term numInCat numDEInCat q.value2
11406 GO:0048710 regulation of astrocyte differentiation 21 0 1
9841 GO:0050804 regulation of synaptic transmission 194 46 1
9840 GO:0050679 positive regulation of epithelial cell proliferation 123 26 1
9838 GO:0071897 DNA biosynthetic process 56 9 1
9834 GO:0060333 interferon-gamma-mediated signaling pathway 72 13 1
9833 GO:2000027 regulation of organ morphogenesis 135 31 1
9839 GO:0017156 calcium ion-dependent exocytosis 43 6 1
10212 GO:0007158 neuron cell-cell adhesion 14 0 1
11456 GO:0051044 positive regulation of membrane protein ectodomain proteolysis 14 0 1
9820 GO:0030030 cell projection organization 991 311 1
9830 GO:0014013 regulation of gliogenesis 52 9 1
9824 GO:0007224 smoothened signaling pathway 105 24 1
9812 GO:0009887 organ morphogenesis 691 210 1
9835 GO:0017158 regulation of calcium ion-dependent exocytosis 23 2 1
9837 GO:0051043 regulation of membrane protein ectodomain proteolysis 18 1 1
9836 GO:0051180 vitamin transport 18 1 1
9796 GO:0000902 cell morphogenesis 993 314 1
9814 GO:0048704 embryonic skeletal system morphogenesis 84 18 1
9794 GO:0002009 morphogenesis of an epithelium 358 104 1
9823 GO:0003341 cilium movement 34 5 1

Positive Effect

Over enriched categories (93)

rowN <- max(minRow, sum(goPos$q.value<=0.05))
cat(kable(goPos[1:rowN,c("category","term","numInCat","numDEInCat","q.value")],format="html"));
category term numInCat numDEInCat q.value
GO:0045333 cellular respiration 158 57 0.0046008
GO:0002376 immune system process 1936 465 0.0046008
GO:0006901 vesicle coating 38 21 0.0046008
GO:0008219 cell death 1751 425 0.0046008
GO:0006900 membrane budding 53 26 0.0046008
GO:0022904 respiratory electron transport chain 105 40 0.0046008
GO:0006119 oxidative phosphorylation 70 30 0.0046008
GO:0007005 mitochondrion organization 298 92 0.0046008
GO:0065003 macromolecular complex assembly 1091 278 0.0046008
GO:0070271 protein complex biogenesis 934 242 0.0046008
GO:0016265 death 1755 425 0.0046008
GO:0022900 electron transport chain 106 40 0.0046008
GO:0000209 protein polyubiquitination 187 64 0.0048910
GO:0006457 protein folding 197 66 0.0061044
GO:0010033 response to organic substance 2043 486 0.0063195
GO:0006461 protein complex assembly 932 240 0.0063195
GO:0015031 protein transport 1320 327 0.0079437
GO:0051641 cellular localization 2267 533 0.0081304
GO:0042773 ATP synthesis coupled electron transport 54 24 0.0081304
GO:0042775 mitochondrial ATP synthesis coupled electron transport 54 24 0.0081304
GO:0032446 protein modification by small protein conjugation 654 177 0.0081658
GO:0055114 oxidation-reduction process 896 229 0.0096656
GO:0008089 anterograde axon cargo transport 23 14 0.0096656
GO:0006950 response to stress 2909 666 0.0096656
GO:0006091 generation of precursor metabolites and energy 394 112 0.0096656
GO:0032268 regulation of cellular protein metabolic process 1414 346 0.0118963
GO:0044267 cellular protein metabolic process 3491 792 0.0120794
GO:0001775 cell activation 767 199 0.0127894
GO:1902591 single-organism membrane budding 34 18 0.0127894
GO:0006783 heme biosynthetic process 21 13 0.0131969
GO:0008104 protein localization 1760 420 0.0137621
GO:0048522 positive regulation of cellular process 3307 749 0.0150345
GO:0042180 cellular ketone metabolic process 211 67 0.0156104
GO:0070647 protein modification by small protein conjugation or removal 731 192 0.0171355
GO:0006779 porphyrin-containing compound biosynthetic process 27 15 0.0180596
GO:1902582 single-organism intracellular transport 1181 291 0.0180596
GO:0060548 negative regulation of cell death 633 167 0.0190653
GO:0033014 tetrapyrrole biosynthetic process 30 16 0.0190653
GO:0035966 response to topologically incorrect protein 140 48 0.0215816
GO:0006986 response to unfolded protein 133 46 0.0232286
GO:0019752 carboxylic acid metabolic process 829 212 0.0234563
GO:0012501 programmed cell death 1539 367 0.0253782
GO:0006915 apoptotic process 1521 363 0.0253782
GO:0015980 energy derivation by oxidation of organic compounds 319 91 0.0275363
GO:1901700 response to oxygen-containing compound 1037 256 0.0278399
GO:0006955 immune response 1137 276 0.0300459
GO:0046907 intracellular transport 1406 338 0.0300459
GO:0042221 response to chemical 2788 632 0.0302603
GO:0048199 vesicle targeting, to, from or within Golgi 28 15 0.0302603
GO:0043066 negative regulation of apoptotic process 585 154 0.0302603
GO:0002474 antigen processing and presentation of peptide antigen via MHC class I 100 36 0.0302603
GO:0051649 establishment of localization in cell 1974 460 0.0302603
GO:0044257 cellular protein catabolic process 485 132 0.0302603
GO:0006417 regulation of translation 249 75 0.0304719
GO:0051188 cofactor biosynthetic process 132 45 0.0311200
GO:0031571 mitotic G1 DNA damage checkpoint 75 29 0.0311200
GO:0033036 macromolecule localization 2032 473 0.0311200
GO:0042744 hydrogen peroxide catabolic process 19 11 0.0324613
GO:0051246 regulation of protein metabolic process 1748 411 0.0324613
GO:0051603 proteolysis involved in cellular protein catabolic process 470 128 0.0325988
GO:0042542 response to hydrogen peroxide 94 34 0.0333546
GO:0045184 establishment of protein localization 1422 340 0.0344944
GO:0033238 regulation of cellular amine metabolic process 76 29 0.0351669
GO:0044819 mitotic G1/S transition checkpoint 76 29 0.0354518
GO:0044783 G1 DNA damage checkpoint 76 29 0.0354518
GO:0043069 negative regulation of programmed cell death 594 155 0.0354518
GO:0051186 cofactor metabolic process 249 74 0.0356678
GO:0044710 single-organism metabolic process 4810 1054 0.0372367
GO:0006521 regulation of cellular amino acid metabolic process 59 24 0.0372632
GO:0042168 heme metabolic process 27 14 0.0376635
GO:0045948 positive regulation of translational initiation 11 8 0.0380831
GO:0070936 protein K48-linked ubiquitination 45 20 0.0395880
GO:0048518 positive regulation of biological process 3684 818 0.0397096
GO:0016567 protein ubiquitination 612 160 0.0397096
GO:0006120 mitochondrial electron transport, NADH to ubiquinone 42 18 0.0397096
GO:0010941 regulation of cell death 1204 290 0.0397096
GO:0009725 response to hormone 667 171 0.0400500
GO:0009060 aerobic respiration 46 20 0.0415735
GO:0002263 cell activation involved in immune response 141 46 0.0415735
GO:0002366 leukocyte activation involved in immune response 141 46 0.0415735
GO:0010035 response to inorganic substance 322 90 0.0429863
GO:0034613 cellular protein localization 1124 273 0.0429863
GO:0010608 posttranscriptional regulation of gene expression 422 115 0.0429863
GO:0010498 proteasomal protein catabolic process 284 82 0.0429863
GO:0036230 granulocyte activation 25 13 0.0429863
GO:0002274 myeloid leukocyte activation 123 41 0.0429863
GO:0070727 cellular macromolecule localization 1129 274 0.0429863
GO:0042590 antigen processing and presentation of exogenous peptide antigen via MHC class I 79 29 0.0454961
GO:0042981 regulation of apoptotic process 1145 276 0.0466301
GO:0033013 tetrapyrrole metabolic process 50 21 0.0487214
GO:0034109 homotypic cell-cell adhesion 68 26 0.0487214
GO:0072329 monocarboxylic acid catabolic process 84 31 0.0494306
GO:0034622 cellular macromolecular complex assembly 583 150 0.0495864

Under enriched (0)

goPos <- goPos[order(goPos$under_represented_pvalue),]
rowN <- max(minRow, sum(goPos$q.value2<=0.05))
cat(kable(goPos[1:rowN,c("category","term","numInCat","numDEInCat","q.value2")],format="html"));
category term numInCat numDEInCat q.value2
8506 GO:0009887 organ morphogenesis 691 100 0.2741585
8508 GO:0042476 odontogenesis 93 5 0.2741585
8507 GO:0042475 odontogenesis of dentin-containing tooth 62 2 0.3986425
8502 GO:0034654 nucleobase-containing compound biosynthetic process 3350 605 0.5533250
8503 GO:0032318 regulation of Ras GTPase activity 318 41 0.5624981
8505 GO:0006415 translational termination 95 6 0.5624981
8494 GO:0032774 RNA biosynthetic process 3063 554 0.6861498
8504 GO:0006614 SRP-dependent cotranslational protein targeting to membrane 107 8 0.6861498
8500 GO:0072599 establishment of protein localization to endoplasmic reticulum 111 9 0.9519174
8498 GO:0007224 smoothened signaling pathway 105 9 0.9519174
8496 GO:0045047 protein targeting to ER 110 9 0.9519174
8495 GO:0006613 cotranslational protein targeting to membrane 109 9 0.9771977
8497 GO:0051101 regulation of DNA binding 67 4 1.0000000
8492 GO:0032320 positive regulation of Ras GTPase activity 266 35 1.0000000
8499 GO:0021510 spinal cord development 57 3 1.0000000
8489 GO:0019438 aromatic compound biosynthetic process 3410 629 1.0000000
8486 GO:0018130 heterocycle biosynthetic process 3413 630 1.0000000
8493 GO:0071897 DNA biosynthetic process 56 3 1.0000000
8501 GO:0048663 neuron fate commitment 38 1 1.0000000
8482 GO:0044271 cellular nitrogen compound biosynthetic process 3463 642 1.0000000

Negative Effect

Over enriched categories (62)

category term numInCat numDEInCat q.value
GO:0006415 translational termination 95 77 0.0000000
GO:0006414 translational elongation 121 87 0.0000000
GO:0006614 SRP-dependent cotranslational protein targeting to membrane 107 78 0.0000000
GO:0072599 establishment of protein localization to endoplasmic reticulum 111 79 0.0000000
GO:0006613 cotranslational protein targeting to membrane 109 78 0.0000000
GO:0045047 protein targeting to ER 110 78 0.0000000
GO:0000184 nuclear-transcribed mRNA catabolic process, nonsense-mediated decay 118 81 0.0000000
GO:0070972 protein localization to endoplasmic reticulum 128 81 0.0000000
GO:0006413 translational initiation 167 92 0.0000000
GO:0019083 viral transcription 158 86 0.0000000
GO:0006612 protein targeting to membrane 171 90 0.0000000
GO:0019080 viral gene expression 168 86 0.0000000
GO:0044033 multi-organism metabolic process 178 86 0.0000000
GO:0043624 cellular protein complex disassembly 174 86 0.0000000
GO:0043241 protein complex disassembly 195 91 0.0000000
GO:0000956 nuclear-transcribed mRNA catabolic process 184 85 0.0000000
GO:0032984 macromolecular complex disassembly 205 91 0.0000000
GO:0090150 establishment of protein localization to membrane 296 112 0.0000000
GO:0006402 mRNA catabolic process 196 86 0.0000000
GO:0006401 RNA catabolic process 222 89 0.0000000
GO:0072657 protein localization to membrane 371 120 0.0000000
GO:0006412 translation 496 140 0.0000000
GO:1902578 single-organism localization 426 127 0.0000000
GO:1902580 single-organism cellular localization 426 127 0.0000000
GO:0019058 viral life cycle 303 98 0.0000000
GO:0022411 cellular component disassembly 412 117 0.0000000
GO:0072594 establishment of protein localization to organelle 456 123 0.0000000
GO:0006605 protein targeting 497 129 0.0000000
GO:0044802 single-organism membrane organization 638 156 0.0000000
GO:0033365 protein localization to organelle 603 145 0.0000001
GO:0061024 membrane organization 778 177 0.0000001
GO:0034645 cellular macromolecule biosynthetic process 3920 684 0.0000038
GO:0032774 RNA biosynthetic process 3063 549 0.0000070
GO:0009059 macromolecule biosynthetic process 4025 695 0.0000132
GO:0034654 nucleobase-containing compound biosynthetic process 3350 589 0.0000210
GO:0019438 aromatic compound biosynthetic process 3410 597 0.0000276
GO:0042254 ribosome biogenesis 167 50 0.0000366
GO:0018130 heterocycle biosynthetic process 3413 596 0.0000379
GO:1901362 organic cyclic compound biosynthetic process 3503 609 0.0000426
GO:0044249 cellular biosynthetic process 4756 800 0.0000444
GO:1901576 organic substance biosynthetic process 4830 810 0.0000523
GO:0044271 cellular nitrogen compound biosynthetic process 3463 602 0.0000523
GO:0042274 ribosomal small subunit biogenesis 21 13 0.0001104
GO:0016071 mRNA metabolic process 615 133 0.0001349
GO:0009058 biosynthetic process 4899 818 0.0001491
GO:0006886 intracellular protein transport 758 159 0.0002299
GO:0006364 rRNA processing 117 36 0.0007890
GO:0071822 protein complex subunit organization 1283 247 0.0009614
GO:0042273 ribosomal large subunit biogenesis 16 10 0.0019875
GO:0016032 viral process 674 139 0.0020435
GO:0043933 macromolecular complex subunit organization 1450 272 0.0021696
GO:0016072 rRNA metabolic process 122 36 0.0021974
GO:0016482 cytoplasmic transport 825 166 0.0022387
GO:0044764 multi-organism cellular process 682 140 0.0023604
GO:0022613 ribonucleoprotein complex biogenesis 280 67 0.0029202
GO:0044403 symbiosis, encompassing mutualism through parasitism 727 145 0.0066024
GO:0044419 interspecies interaction between organisms 727 145 0.0066024
GO:0000028 ribosomal small subunit assembly 7 6 0.0074772
GO:0070727 cellular macromolecule localization 1129 215 0.0086284
GO:0034613 cellular protein localization 1124 213 0.0128879
GO:0090304 nucleic acid metabolic process 4166 691 0.0137670
GO:0016070 RNA metabolic process 3693 619 0.0144945

Under enriched (0)

category term numInCat numDEInCat q.value2
7244 GO:0044092 negative regulation of molecular function 778 77 0.3556853
7241 GO:0001775 cell activation 767 78 0.3556853
7243 GO:0060560 developmental growth involved in morphogenesis 127 6 0.3556853
7240 GO:0044257 cellular protein catabolic process 485 46 0.3556853
7239 GO:0010035 response to inorganic substance 322 26 0.3556853
7238 GO:0098602 single organism cell adhesion 327 28 0.3556853
7231 GO:0006508 proteolysis 1113 126 0.3556853
7232 GO:0043086 negative regulation of catalytic activity 605 60 0.3556853
7233 GO:0051603 proteolysis involved in cellular protein catabolic process 470 45 0.3556853
7236 GO:0016337 single organismal cell-cell adhesion 283 23 0.3556853
7234 GO:0048002 antigen processing and presentation of peptide antigen 180 11 0.4507919
7242 GO:0006888 ER to Golgi vesicle-mediated transport 63 1 0.4792202
7225 GO:0019941 modification-dependent protein catabolic process 433 42 0.5572191
7228 GO:0019882 antigen processing and presentation 215 15 0.5572191
7222 GO:0022610 biological adhesion 916 106 0.5572191
7218 GO:0002376 immune system process 1936 238 0.5572191
7230 GO:0002474 antigen processing and presentation of peptide antigen via MHC class I 100 4 0.5572191
7219 GO:0007155 cell adhesion 912 106 0.5572191
7223 GO:0048589 developmental growth 250 21 0.5572191
7237 GO:0008625 extrinsic apoptotic signaling pathway via death domain receptors 72 2 0.5572191

Final Step: csv output

write.csv(go,file=paste("FDR/csv/", outFile,"_main.csv",sep=''), row.names=FALSE)

## Warning in file(file, ifelse(append, "a", "w")): cannot open file 'FDR/csv/
## bmi_main.csv': No such file or directory

## Error in file(file, ifelse(append, "a", "w")): cannot open the connection

write.csv(goPos,file=paste("FDR/csv/", outFile,"Pos.csv",sep=''), row.names=FALSE)

## Warning in file(file, ifelse(append, "a", "w")): cannot open file 'FDR/csv/
## bmiPos.csv': No such file or directory

## Error in file(file, ifelse(append, "a", "w")): cannot open the connection

write.csv(goNeg,file=paste("FDR/csv/", outFile,"Neg.csv",sep=''), row.names=FALSE)

## Warning in file(file, ifelse(append, "a", "w")): cannot open file 'FDR/csv/
## bmiNeg.csv': No such file or directory

## Error in file(file, ifelse(append, "a", "w")): cannot open the connection