Question: Puzzled by GOseq analyses
gravatar for T_18
14 months ago by
T_1840 wrote:

Dear all,

I am currently trying to run a GO enrichment analysis using GOseq but I am slightly puzzled if I am doing things correctly given my (zero) output. My endgoal is to get results I can use in GOgadget.

I have the following files: - Factor labels (either differently expressed or not, so two groups) - Gene lenghts file - GO annotations linked to the gene IDs

However calculating pwf results in the following warning:

Warning message: In newton(lsp = lsp, X = G$X, y = G$y, Eb = G$Eb, UrS = G$UrS, L = G$L, : Fitting terminated with step failure - check results carefully

I created a plot showing the "proportion of DE", like on page 8 of the GOseq manual. I get a flat line on 0. Meaning that there is no significant difference?

Does anyone know what potentially could be the problem here?

goseq gogadget R • 417 views
ADD COMMENTlink written 14 months ago by T_1840

Can you provide the code, and plot? I think the failure is the reason why you have a flat line, do you have RNAseq data?

ADD REPLYlink written 14 months ago by Benn7.8k

Yes, it's RNAseq data. I'm currently home, but will provide the code when I'll be in the office tomorrow. Thanks so far.

ADD REPLYlink written 14 months ago by T_1840
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