[BioC] Top gene list
daphne mouzaki (RI)
daphne.mouzaki at bbsrc.ac.uk
Thu Sep 14 14:13:18 CEST 2006
Hi and thanks for your response,
actually topTable and Write.fit works if the object that I have is a
MArrayLM object but.
The problem is that I have an object "Bgene" which is a list and
includes all the columns of interest.I am sorry that I wasn't clear.I
have already generated the results but I also tried decideTests in case
I could generated them in an other way to get all the FDRs and fold
changes for each gene.
 "ttAll" "DownSameUp"
 "T11" "T3" "T19" "T19_T11"
 "Row" "Column" "Block" "Name" "ID"
 "Reps" "ARKcloneID" "Status" "M" "A"
 "t" "P.Value" "adj.P.Val" "B" "FoldChange"
 "FDRmax" "FDR" "FDRup" "FDRlow"
For example, I want to get all the FDr for time point T11 with the
respective gene name FDR11<-(Bgene$ttAll[])$FDRmax
the problem is that I don't get the respective gene names automatically
when I do that and when I assign
rownames(FDR)<-sort(unique(MA$genes$ARKcloneID)) I get an error message
that I assign it to something with no dimension which is true because it
is not a matrix but a list!!
From: Giovanni Coppola [mailto:gcoppola at ucla.edu]
Sent: 13 September 2006 17:40
To: daphne mouzaki (RI)
Cc: Bioconductor list
Subject: Re: [BioC] topTable gene list
perhaps ?write.fit does what you want.
On Sep 13, 2006, at 7:13 AM, daphne mouzaki ((RI)) wrote:
> I have generated a list of significant genes for 3 time points
> separately using the function "decideTests"in Limma package.Using this
> function I generated foldchanges and FDR for every gene using method
> Benjamini and Hochberg ("BH") and p.value=0.05.
> I was wondering if it is possible to generate all the FDR and
> foldchanges with the respective gene name for every time point.
> I tried changing the cut-off to 1 in order not to exclude anything and
> the method set to the function "decideTests" changed to "none" but it
> doesn't work.
> Could you recommend any other possible ways?
> I would appreciate any help,
> Bioconductor mailing list
> Bioconductor at stat.math.ethz.ch
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