[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.

> class(Bgene)
[1] "list"
> names(Bgene)
[1] "ttAll"      "DownSameUp"
> names(Bgene$ttAll)
[1] "T11"     "T3"      "T19"     "T19_T11"
> names(Bgene$ttAll[1])
[1] "T11"
> names(Bgene$ttAll[[1]])
 [1] "Row"        "Column"     "Block"      "Name"       "ID"        
 [6] "Reps"       "ARKcloneID" "Status"     "M"          "A"         
[11] "t"          "P.Value"    "adj.P.Val"  "B"          "FoldChange"
[16] "FDRmax"     "FDR"        "FDRup"      "FDRlow"

For example, I want to get all the FDr for time point T11 with the
respective gene name FDR11<-(Bgene$ttAll[[1]])$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!! 



-----Original Message-----
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

Hi Daphne,
perhaps ?write.fit does what you want.

On Sep 13, 2006, at 7:13 AM, daphne mouzaki ((RI)) wrote:

> hi,
> 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,
> Daphne
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