Question: Puzzled by GOseq analyses
gravatar for T_18
8 months ago by
T_1830 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 • 271 views
ADD COMMENTlink written 8 months ago by T_1830

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 8 months ago by Benn6.6k

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 8 months ago by T_1830
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