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 logFClogCPMLR 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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