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3 months ago
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I am new to R and when using the WGCNA pipeline I encounter this message error that I can not seem to solve:
Error in WGCNA::goodGenes(datExpr, ...) : Too few genes with valid expression levels in the required number of samples.
I have already looked more in depth at the
goodGenes() code using trace function but it does not help me in knowing why my genes are not valid. Furthermore it seems that the paper about WGCNA does not mention the
Could anyone explain to me the
goodGenes function and why my genes are not valid?
According to description : "This function checks data for missing entries and returns a list of genes that have non-zero variance and pass two criteria on maximum number of missing values and values whose weight is below a threshold: the fraction of missing values must be below a given threshold and the total number of present samples must be at least equal to a given threshold. If weights are given, entries whose relative weight is below a threshold will be considered missing."
You may need to double check your input data for missing values
Hi Basti thanks for your reply, I will look more into it.
did you solve the problem?
Hi For now I have solved it by lowering the default parameter minNSamples since I have a small dataset but no missing values in it
Ok, keep in mind that you need at least 15 samples to run WGCNA
If you wanted to reproduce their results exactly their code is a bit confusing and there seems to be a mismatch between the function description and code, but a simple/inexact approximation to start off would be filtering out genes with zero variance, and genes with counts greater than zero in less than half the samples.