Error in SAMseq analysis with R
I am trying to use the function SAMseq from samr package to analyse the gene expression of my matrix but I get this error message.
> sam_test = SAMseq(RNA_seq_DNAm, vector_DNAm, resp.type = "Quantitative",
genenames = names)
Estimating sequencing depths...
Resampling to get new data matrices...
Error in rankcol(t(xresamp[, , k])) :
NA/NaN/Inf in foreign function call (arg 1)
In addition: There were 20 warnings (use warnings() to see them)
Error during wrapup: cannot open the connection
Can someone help me understand what it means? This is a school project I am working on.
Thanks in advance!
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namilio06 •
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Since the error appears to result from some non-numeric or non-finite values, first thing you might want to try is to check for those in your input counts, e.g.:
sapply(RNA_seq_DNAm, function(x) { sumis.na(x)) })for NAs. You can modify this to check for NaN's (is.nan) or Infs (abs(x) == Inf).I am experiencing the same problem. Any resolution for that?