[BioC] new error: when running gage

[Luo Weijun]

Hi Sohail,
When you deal with single column/experiment data, you should set heatamp argument to FALSE in sigGeneSet function. There is no sense to generate heatmap for single column data, right? The message you’ve got is actually not error but warning message when you tried generating heamap for such data. The following example run with single-column/experiment data work well. You may want to try your analysis again with the correct setting. Notice that you need to update your gage package to the development version at http://bioconductor.org/packages/2.9/bioc/html/gage.html. There are some bug when running gage 2.2.x with single column data. HTH.
Weijun

library(gage)
library(gageData)
data(gse16873)
#gene sets data available for other species, type in ?kegg.gs
data(kegg.gs)

#single column data without control
gse16873.kegg.p <- gage(gse16873[,1], gsets = kegg.gs)
#single experiment data with control
gse16873.kegg.2.p <- gage(gse16873, ref=1, samp=3, gsets = kegg.gs)

#extract significant gene set results
gse16873.kegg.sig=sigGeneSet(gse16873.kegg.p, heatmap=F)
gse16873.kegg.2d.sig=sigGeneSet(gse16873.kegg.p, heatmap=F)






On 5/4/2011 3:47 PM, sohkhan at notes.cc.sunysb.edu wrote:
> Hi Weijun,
> 
> I getting the following error: when I use the function sigGeneSet()
> 
> analysis_4_vs_1.sig=sigGeneSet(analysis_4_VS_1,outname="4_VS_1",heatmap=T)
> [1] "gs.data needs to be a matrix-like object!"
> [1] "No heatmap produced for down-regulated gene sets, only 1 or none 
> signficant."
> [1] "gs.data needs to be a matrix-like object!"
> [1] "there are 8 significantly up-regulated gene sets"
> [1] "there are 0 significantly down-regulated gene sets"
> 
> analysis_4_VS_1 is my output from gage(), which is a "list"
> In addition heatmap pdfs are created, but can't open them......get an 
> error the file format is unrecognizable.
> 
> How can I just get significant list for up and down....gene sets?
> 
> Do you prefer I ask questions regarding "gage" on the Bioconductor list 
> in the future?
> Thanks.
> 
> -Sohail