Hello all, I am receiving an error message in DESeq which I do not understand. I have data from 14 samples (7 samples for condition A and 7 samples for condition B). If I run DESeq on all samples, it works without error messages. However, if I just choose a subset of the samples (3 samples for condition A and 3 samples for condition B), it may or may not work, depending on the subset.
When trying to run estimateVarianceFunctions(cds), I get the following error message and no variance functions are added:
I have not been able to figure out where the function encounters these NA/NaN/Inf values and what could be done to make it work. Does anyone have suggestions?
In addition, the size factors are all estimated to 1. This seems to cause the following warnings:
It does not appear to me that this is the culprit that causes the variance function estimation to fail, but I may be wrong.
Any help is appreciated.
Regards,
aquila
When trying to run estimateVarianceFunctions(cds), I get the following error message and no variance functions are added:
Code:
Error in preplot.locfit.raw(object, newdata, where, what, band) : NA/NaN/Inf in foreign function call (arg 2)
In addition, the size factors are all estimated to 1. This seems to cause the following warnings:
Code:
1: In lfproc(x, y, weights = weights, cens = cens, base = base, geth = geth, : compparcomp: perfect fit 2: In lfproc(x, y, weights = weights, cens = cens, base = base, geth = geth, : procv: parameters out of bounds
Any help is appreciated.
Regards,
aquila
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