[BioC] topTable changes

[J.delasHeras at ed.ac.uk]

Quoting Sue Jones <s.jones at sussex.ac.uk>:

>
>
> I have used the following code to find differentially expressed genes
> : based on affymetrix data when treating cells with water (controls) and
> ethanol (treatment).
>
> files <- c("W05h_1.CEL", "W0h_1.CEL", "W2h_1.CEL",
> "W2h_2.CEL", "W4h_1.CEL",  "E2h_1.CEL",  "E2h_2.CEL",
> "E2h_3.CEL", "E2h_4.CEL")
> Data <- ReadAffy(filenames = files)
> Data_gcrma <- gcrma(Data)
> design<- cbind(WAT=c(1,1,1,1,1,0,0,0,0), ETH=c(0,0,0,0,0,1,1,1,1))
> design
>
> fit <- lmFit(Data_gcrma,design)
> cont.matrix <- makeContrasts(WATvsETH=ETH-WAT, levels=design)
> fit2<- contrasts.fit(fit,cont.matrix)
> fit3 <- eBayes(fit2)
>
> tab <- topTable(fit3, n=1500, adjust="fdr")
> genenames <- as.character(tab$ID)
> ll <- getLL(genenames, "drosgenome1")
> sym <- getSYMBOL(genenames, "drosgenome1")
> tab2 <- data.frame(sym,tab)
>
> diff_exp <- tab2[tab2$P<0.05 & tab2$M<0.0,]
> print("No down reg genes:"); length(diff_exp$ID)
>
> diff_exp <- tab2[tab2$P<0.05 & tab2$M>0.0,]
> print("No up reg genes:") ;length(diff_exp$ID)
>
>
> The question I have is about the topTable function. Does this now only
> produce a P.value column which contains the adjusted P-values and is this
> column tagged as "P"? Are the two lines of code that extract the genes
> with P values <0.05 correct?
>
> diff_exp <- tab2[tab2$P<0.05 & tab2$M<0.0,]
> print("No down reg genes:"); length(diff_exp$ID)
>
>
> previously I had code which used $adj.P.Val as a filter but this does not
> work any more.
>
> Thanks
>
> Sue Jones
> University of Sussex

Not sure which version of Limma you're using, but since version 2.9.3  
(Oct'06)topTable has changed a couple of column headings: "M" is  
"logFC" now, and you're using "M" that on your code, so I think this  
may be the problem.

You can use changeLog() to see changes in Limma.

Jose


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Dr. Jose I. de las Heras                      Email: J.delasHeras at ed.ac.uk
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