The editor has been updated to markdown! Please see more info at: Tutorial: Updated Support Site Editor

Question: new error: when running gage
gravatar for Luo Weijun
7.8 years ago by
Luo Weijun1.4k
United States
Luo Weijun1.4k wrote:
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 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 ? #single column data without control gse16873.kegg.p <- gage(gse16873[,1], gsets = #single experiment data with control gse16873.kegg.2.p <- gage(gse16873, ref=1, samp=3, gsets = #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 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",heat map=T) > [1] " needs to be a matrix-like object!" > [1] "No heatmap produced for down-regulated gene sets, only 1 or none > signficant." > [1] " 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
gage • 728 views
ADD COMMENTlink written 7.8 years ago by Luo Weijun1.4k
Please log in to add an answer.


Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 16.09
Traffic: 319 users visited in the last hour