GOseq output but strange warning message!
Entering edit mode
TB18 • 0
Last seen 5.8 years ago


Dear all,

I am running GOseq on a custom annotated dataset. I am getting a nicely looking output: list of enriched and depleted GOterms for my different groups, just as I want. But after calculating pwf I get the following warning message:

> pwf=nullp(cat_genes_vec,bias.data=lengths_features_with_GO)
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​

But pwf is calculated:

> head(pwf)
  DEgenes bias.data         pwf
1       0       243 0.001000788
2       0       560 0.001000780
3       0       262 0.001000788
4       0      1176 0.001000628
5       0       248 0.001000788
6       0       291 0.001000788

Further, the plot from nullp is just a flat line on 0 (or more likely 0.001) hard to tell. I cannot clarify this. I think the warning message and plot result are related; I do get an output when I continue. 

Can someone help me understanding this?

Thanks in advance!

GOseq GO pwf goseq • 1.2k views
Entering edit mode

Hi there. I am getting the same warning message while executing broadenrich() for GO and KEGG pathway enrichment.


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