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Forum: Bioinformatics 07-17-2014, 12:49 PM
Replies: 92
Views: 38,219
Posted By tigerxu
I very appreciate your information! Very helpful...

I very appreciate your information! Very helpful to further my understanding on the statistical background of GAGE.
Forum: Bioinformatics 07-11-2014, 12:26 PM
Replies: 92
Views: 38,219
Posted By tigerxu
I have followed the default workflows of gage and...

I have followed the default workflows of gage and pathview on the example RNA-seq dataset. I also used the fold changes inferred by deseq2, then followed by the gage and pathview. I found both...
Forum: Bioinformatics 07-10-2014, 06:26 AM
Replies: 92
Views: 38,219
Posted By tigerxu
Okay, thank! I will try version 2.14.3 later.

Okay, thank! I will try version 2.14.3 later.
Forum: Bioinformatics 07-09-2014, 10:39 AM
Replies: 92
Views: 38,219
Posted By tigerxu
The problem is still there. But I have modified...

The problem is still there. But I have modified the margins parameters in the internal function sigGeneSet within the gage package. It can work!
Forum: Bioinformatics 07-09-2014, 03:06 AM
Replies: 92
Views: 38,219
Posted By tigerxu
other attached packages: [1] gage_2.14.2 ...

other attached packages:
[1] gage_2.14.2 GenomicAlignments_1.0.2
[3] BSgenome_1.32.0 Rsamtools_1.16.1
[5] Biostrings_2.32.0 XVector_0.4.0 ...
Forum: Bioinformatics 07-07-2014, 03:13 AM
Replies: 92
Views: 38,219
Posted By tigerxu
I have a question about the margin argument in...

I have a question about the margin argument in the sigGeneSet function when I run the following command
> rcount.kegg.sig<-sigGeneSet(rcount.kegg.p, outname="sig.kegg",pdf.size=c(7,12),margins=c(5,...
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