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Description
I am running into a problem when I am running ImSig. My input file is a normalized counts file that has HGNC gene symbols in the first column, and normalized read counts for each of my samples. I have followed the Github tutorial in running ImSig in R. I have changed the first column to rownames and my file looks like the example data set built into ImSig from what I can tell. Yet, when I run ImSig I am getting the following error:
imsig(Norm_TME_Alone_KRAS)
---> Checking zero-variance data...
---> Total number of variables: 34
---> WARNING: 2 variables found with zero variance
---> Checking zero-variance data...
---> Total number of variables: 63
---> WARNING: 2 variables found with zero variance
---> Checking zero-variance data...
---> Total number of variables: 75
---> WARNING: 4 variables found with zero variance
---> Checking zero-variance data...
---> Total number of variables: 36
---> WARNING: 3 variables found with zero variance
---> Checking zero-variance data...
---> Total number of variables: 43
---> WARNING: 4 variables found with zero variance
---> Checking zero-variance data...
---> Total number of variables: 14
---> WARNING: 4 variables found with zero variance
---> Checking zero-variance data...
---> Total number of variables: 11
---> WARNING: 3 variables found with zero variance
---> Checking zero-variance data...
---> Total number of variables: 97
---> WARNING: 97 variables found with zero variance
---> Maximum number of splits: floor(n/2) = 0
---> WARNING: number of splits nSplit > 0
---> WARNING: using maximum number of splits: nSplit = 0
Error in fastCor(t(exp)) : invalid nSplit: 0
I am unable to determine what is going wrong, and what I need to change. Here is an example of the first few lines of my data frame.
