WGCNA dealing with missing data

Question

[nazaninhoseinkhan]

Dear all,

I have run WGCNA and in the first step of it I tried to remove samples with too many missing values using the following code:

gsg = goodSamplesGenesMS(multiExpr, verbose = 3);

gsg$allOK

if (!gsg$allOK) {

Print information about the removed genes:

if (sum(!gsg$goodGenes) > 0)

printFlush(paste("Removing genes:", paste(names(multiExpr[[1]]$data)[!gsg$goodGenes],

collapse = ", ")))

for (set in 1:exprSize$nSets)

{ if (sum(!gsg$goodSamples[[set]]))

printFlush(paste("In set", setLabels[set], "removing samples",

paste(rownames(multiExpr[[set]]$data)[!gsg$goodSamples[[set]]], collapse = ", ")))

Remove the offending genes and samples

multiExpr[[set]]$data = multiExpr[[set]]$data[gsg$goodSamples[[set]], gsg$goodGenes];

}

Update exprSize

exprSize = checkSets(multiExpr) }

I want to know what is the cutoff of WGCNA for missing data to remove a sample?

In the tutorial of WGCNA it has mentioned that samples with too many missing data will be removed, but not mentioned exactly the used cutoff.

I will appreciate any help

Nazanin

Answer 1

[Jake Warner]

Hi. You can designate the cutoffs with the minFraction and or minNsamples arguments. https://www.rdocumentation.org/packages/WGCNA/versions/1.41-1/topics/goodSamplesGenesMS