[BioC] topTable threshold on p-value and logFC [Re: was design matrix]

[Gordon Smyth]

I have changed the subject line to something more appropriate.

In R 2.5.1 and Bioconductor 2.0, the recommended way to do what you 
want (select DE genes on the basis of a combination of p-value and 
log fold change) was to use decideTests(). In R 2.6.0 and 
Bioconductor 2.1, you will find that topTable() now has p-value and 
logFC arguments which allow you to do the same thing using topTable().

Best wishes
Gordon

>Date: Wed, 3 Oct 2007 17:31:34 +0100 (BST)
>From: Lev Soinov <lev_embl1 at yahoo.co.uk>
>Subject: Re: [BioC] design matrix
>To: "James W. MacDonald" <jmacdon at med.umich.edu>
>Cc: bioconductor at stat.math.ethz.ch
>Message-ID: <412385.24484.qm at web27908.mail.ukl.yahoo.com>
>Content-Type: text/plain
>
>Dear List,
>
>   Could you help me with another small issue?
>   I usually write out the results of my analysis using the 
> write.table function as follows:
>
>   Assuming 30000 probes in the dataset:
>   data <- ReadAffy()
>   eset <- rma(data)
>
>   design <- model.matrix(~ -1+factor(c(1,1,1,2,2,3,3,3)))
>   colnames(design) <- c("group1", "group2", "group3")
>   contrast.matrix <- makeContrasts(group2-group1, group3-group2, 
> group3-group1, levels=design)
>
>   fit <- lmFit(temp, design)
>   fit2 <- contrasts.fit(fit, contrast.matrix)
>   fit2 <- eBayes(fit2)
>
>   C1<-topTable(fit2, coef=1, number=30000, adjust="BH")
> 
>write.table(C1,file="comparison1.txt",append=TRUE,quote=FALSE,sep="\t",row.names=TRUE,col.names=FALSE)
>
>   C2<-topTable(fit2, coef=2, number=30000, adjust="BH")
> 
>write.table(C2,file="comparison2.txt",append=TRUE,quote=FALSE,sep="\t",row.names=TRUE,col.names=FALSE)
>
>   C3<-topTable(fit2, coef=3, number=30000, adjust="BH")
> 
>write.table(C3,file="comparison3.txt",append=TRUE,quote=FALSE,sep="\t",row.names=TRUE,col.names=FALSE)
>
>   I then use the written out txt files (comparison1.txt, 
> comparison2.txt and comparison3.txt) to select significant probes 
> on the basis of log2fold change and adjusted p values thresholds, using Excel.
>   Would you say that this is a correct way to do this and could you 
> please recommend me some other, may be more efficient way of 
> writing the results of topTable for all 30000 probes out?
>
>   With kind regards,
>   Lev.