On 08/24/2013 04:50 AM, Robin Mjelle wrote:> 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)
edgeR is a Bioconductor package, so please ask on their mailing list (no
subscription required!)
http://bioconductor.org/help/mailing-list/
Remember to provide a reproducible example (people on the list will not be able
to created your 'data' object; perhaps working with the simulated data
on the
help page ?glmFit is a good place to start?) and to include the output of
sessionInfo() so that there is no ambiguity about the software version you are
using.
Martin
>
>
> 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
>
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>
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