Hello all,
I've been using SPIA (Signal Pathway Impact analysis), and I think its great. I'm surprised I don't see it up on the forum more often, and I thought I would start this thread, one to discuss it and how to use it, and two, how DESeq (which I'm guessing most of us would be using if we were to use SPIA) works with it.
Let me start off about DESeq. So when I write my res file that I generate from DESeq, I get entries that are Inf or #Name when one gene doesn't have any transcripts. SPIA doesn't know how to handle these and it crashes. So far, I've just been manually changing it (I guess I could use R) to numbers on the higher end. Does anyone else have a more scientific solution?
Also my annotation gtf is of gene names for human, hg19. SPIA only uses ENTREZ gene IDs. So I convert them using Clone|Gene ID converter (this gets maybe 70% of them). Does anyone have a gtf file that uses just ENTREZ gene IDs or knows where I can get one?
I've been using SPIA (Signal Pathway Impact analysis), and I think its great. I'm surprised I don't see it up on the forum more often, and I thought I would start this thread, one to discuss it and how to use it, and two, how DESeq (which I'm guessing most of us would be using if we were to use SPIA) works with it.
Let me start off about DESeq. So when I write my res file that I generate from DESeq, I get entries that are Inf or #Name when one gene doesn't have any transcripts. SPIA doesn't know how to handle these and it crashes. So far, I've just been manually changing it (I guess I could use R) to numbers on the higher end. Does anyone else have a more scientific solution?
Also my annotation gtf is of gene names for human, hg19. SPIA only uses ENTREZ gene IDs. So I convert them using Clone|Gene ID converter (this gets maybe 70% of them). Does anyone have a gtf file that uses just ENTREZ gene IDs or knows where I can get one?
Comment