[BioC] issue on removing all NAs (UNANNOTATED) rows

[Guest [guest]]

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.sig.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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