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Invalid row.names length error (scde.error.models) #7
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Hi Jens, It's a bit hard for us to tell what's going on without a trackback. The easiest way may be for you to share your count table with me (text table or RData) if that's possible. You can email me at jeanfan@broadinstitute.org. Let me know. Thanks! Best, |
Hi all, I could solve the issue by running a freshly compiled R-3.2.1: locale: attached base packages: other attached packages: loaded via a namespace (and not attached): The issue above was due to my environment, but I couldn't figure out what exactly caused it. |
Thanks, Jens! Glad it worked out. |
Hi all,
when running scde.error.models on a count table with raw counts, I get the following error after several "Classification:weighted" messages:
Error in
row.names<-.data.frame
(*tmp*
, value = value) : invalid 'row.names' lengthhead(ct) looks like:
X94_S62 X43_S29 X53_S32 X32_S22 X58_S35 X27_S18 X73_S47 X63_S38 X83_S55 X88_S59
ENSMUSG00000030105 2 5 72 0 0 34 0 0 0 0
ENSMUSG00000098001 0 0 0 0 0 0 0 0 0 0
ENSMUSG00000065904 0 0 0 0 0 0 0 0 0 0
ENSMUSG00000058979 0 0 0 0 73 0 0 0 0 0
ENSMUSG00000049536 0 0 1 645 0 0 0 0 0 0
ENSMUSG00000027333 0 0 0 0 0 0 0 0 0 0
The initial call was
o.ifm = scde.error.models(counts=ct,n.cores = n.cores, threshold.segmentation = T, save.crossfit.plots = F, save.model.plots = F, verbose = 1)
I can provide the full count table if neccessary. Maybe someone can point me in a direction :)
Best
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