[BioC] edgeR annotation mission from topTags output
R [guest]
guest at bioconductor.org
Sun Aug 25 22:25:41 CEST 2013
after updating R and edgeR I lost the annotations in the final Diff.Expressed matrix (toptags) when running the edgeR pipeline. How do I get the row.names from the data matrix into the topTag-matrix?
data <- read.table("KO_and_WT_Summary_miRNA_Expression.csv", row.names=1, sep="", header=T)
head(data)
T0h T0.25h T0.5h T1h T2h T3h T6h T12h T24h T48h C0h C0.25h
mmu-let-7a-1-3p 450 329 395 300 469 320 245 281 300 376 166 242
mmu-let-7a-5p 93070 62871 65013 69714 73983 60836 49885 63788 62161 65595 48525 32111
mmu-let-7c-2-3p 436 325 391 295 466 314 243 278 300 376 152 220
mmu-let-7c-5p 544 367 350 492 331 266 323 309 403 613 255 219
mmu-let-7d-3p 7397 5854 5280 6883 5021 5117 5327 6137 5649 5197 6460 3951
mmu-let-7d-5p 8893 7584 7082 8062 6258 6423 6120 7053 7000 6998 7265 3712
keep <- rowSums(cpm(data)>2) >=2
data <- data[keep, ]
table(keep)
y <- DGEList(counts=data[,1:18], genes=data[,0:1])
y <- calcNormFactors(y)
y$samples
plotMDS(y,main="")
Time=c("0.25h","0.5h","1h","2h","3h","6h","12h","24h","48h","0.25h","0.5h","1h","2h","3h","6h","12h","24h","48h")
Condition=c("KO","KO","KO","KO","KO","KO","KO","KO","KO","WT","WT","WT","WT","WT","WT","WT","WT","WT")
design <- model.matrix(~0+Time+Condition)
rownames(design) <- colnames(y)
y <- estimateGLMCommonDisp(y, design, verbose=TRUE, method="deviance",robust=TRUE, subset=NULL)
y <- estimateGLMTrendedDisp(y, design)
y <- estimateGLMTagwiseDisp(y, design)
fit <- glmFit(y, design)
lrt <- glmLRT(fit)
topTags(lrt)
Coefficient: ConditionWT
genes logFC logCPM LR PValue FDR
189 5128 -11.028422 7.905804 4456.297 0 0
188 12271 -10.582267 9.061326 5232.075 0 0
167 121120 -9.831894 12.475576 5957.104 0 0
34 255235 -9.771266 13.592968 7355.592 0 0
168 311906 -9.597952 13.907951 10710.111 0 0
166 631262 -9.592550 14.932018 11719.222 0 0
79 79 9.517226 11.466696 7964.269 0 0
169 2512 -8.946429 6.758584 2502.548 0 0
448 3711 -7.650068 7.764682 2914.784 0 0
32 260769 -7.412197 13.633352 4906.198 0 0
-- output of sessionInfo():
> sessionInfo()
R version 3.0.1 (2013-05-16)
Platform: x86_64-pc-linux-gnu (64-bit)
locale:
[1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C LC_TIME=en_US.UTF-8
[4] LC_COLLATE=en_US.UTF-8 LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8
[7] LC_PAPER=C LC_NAME=C LC_ADDRESS=C
[10] LC_TELEPHONE=C LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
attached base packages:
[1] splines stats graphics grDevices utils datasets methods base
other attached packages:
[1] reshape2_1.2.2 ggplot2_0.9.3.1 edgeR_3.2.4 limma_3.16.7
loaded via a namespace (and not attached):
[1] colorspace_1.2-2 dichromat_2.0-0 digest_0.6.3 grid_3.0.1
[5] gtable_0.1.2 labeling_0.2 MASS_7.3-26 munsell_0.4.2
[9] plyr_1.8 proto_0.3-10 RColorBrewer_1.0-5 scales_0.2.3
[13] stringr_0.6.2 tools_3.0.1
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