[BioC] DESeq Question
anders at embl.de
Wed Mar 21 15:18:37 CET 2012
On 03/21/2012 12:26 AM, Omar Darwish wrote:
> I used the following commands to find the differentially expressed genes.
> I have two questions,
> 1. Are the following commands correct ? or am i missing something?
Yes, except for two oddities:
> libsizes<- clibsizes<- c(X.1=18143070, X.2=13544150, Y.1=17853990,
> sizeFactors(cds)<- libsizes[-1]
> cds<- estimateSizeFactors( cds )
Why do you set the size factors manually, and the use
'estimateSizefactors' to overwrite this information? The first two
commands are gratuitous (and don't even work becaus of the "[-1]"). Omit
> resSig<- res[ res$padj< .001, ]
Do your really want an FDR of only 0.1%? This is extremely stringent. Do
you have any reason for this unusual choice?
> 2. How can i determine which genes are differentially expressed?
> induced? suppressed? unchanged?
Those with and adjusted p value (column "padj") below your chosen FDR
threshold are significant, and the column "log2FoldChange" tells you the
log2 fold change and hence whether they are up- or downregulated.
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