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Last seen 9.6 years ago
Hi,
I am using limma package on HuGene2.0st array. When I tried to remove
the unannotated rows (NAs) after mapping probeID to gene names. Some
significant gene lists I got have the differentially expressed genes,
but some of gene lists have all of the unsignificantly expressed
genes.
The code I used as follows:
cont.matrix <- makeContrasts(
interaction=(T.Ko-T.wt)-(ctrl.Ko-ctrl.wt),
levels=design)
fit2 <- contrasts.fit(fit, cont.matrix)
fit2 <- eBayes(fit2)
sig.interaction = topTable(fit2, coef = "interaction",
number=nrow(fit2), p.value=0.05, lfc=1)
interaction.ids=sig.interaction[["ID"]]
## map probe ids to gene names...
interaction.sig.SYMBOL=mget(interaction.ids,
hugene20sttranscriptclusterSYMBOL, ifnotfound=NA)
#REMOVE ALL NAs (UNANNOTATED) ROWS and unlist them for easy formatting
later
interaction.sig.ann=unlist(interaction.sig.SYMBOL[!is.na(interaction.s
ig.SYMBOL)])
Does anyone know what's wrong with the code? No error message. Any
input is appreciated.
Thanks,
-- output of sessionInfo():
> sessionInfo()
R version 3.0.0 (2013-04-03)
Platform: x86_64-apple-darwin10.8.0 (64-bit)
locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
attached base packages:
[1] stats graphics grDevices utils datasets methods base
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