Question: WGCNA's function goodSampleGenes
0
gravatar for cgias
3 months ago by
cgias0
cgias0 wrote:

Hi,

I'm running WGCNA to my RNA-seq data following the UCLA tutorial by the authors of the package but I'm going through a small issue when checking for excessive missing values and identification of outliers in my sample.

The script in the tutorial is

gsg = goodSamplesGenes(datExpr0, verbose = 3);
gsg$allOK
# if FALSE:
if (!gsg$allOK)
{
# Optionally, print the gene and sample names that were removed:
if (sum(!gsg$goodGenes)>0)
printFlush(paste("Removing genes:", paste(names(datExpr0)[!gsg$goodGenes], collapse = ", ")));
if (sum(!gsg$goodSamples)>0)
printFlush(paste("Removing samples:", paste(rownames(datExpr0)[!gsg$goodSamples], collapse = ", ")));
# Remove the offending genes and samples from the data:
datExpr0 = datExpr0[gsg$goodSamples, gsg$goodGenes]
}

It shows me the info that must be removed but at the end there are a lot of "NA" columns that aren't at the original data (datExpr0 - I've checked it).

[...] LOC110812820, LOC110814046, LOC110812396, LOC110814102, LOC110814183, LOC110814197, LOC110814177, LOC110814128, LOC110814152, LOC110812490, LOC110814289, LOC110814288, LOC110814252, LOC110814293, LOC110814359, LOC110814411, LOC110814324, LOC110814352, LOC110814327, LOC110814437, LOC110814361, LOC110813173, LOC110814443, LOC110814441, LOC110814528, LOC110814501, LOC110814526, LOC110814495, LOC110814487, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA

So obviously when running the last line of the script where it says to actually remove them from the data I get the following error:

Error in `[.data.frame`(datExpr0, gsg$goodSamples, gsg$goodGenes) : 
  undefined columns selected

I've found nothing online about such error so, does anybody have a clue about what's possibly going on?

Thanks in advance,

ADD COMMENTlink modified 11 weeks ago by Biostar ♦♦ 20 • written 3 months ago by cgias0

I just ran the same tutorial and allOK was TRUE. Please verify that you downloaded and loaded the test data: https://horvath.genetics.ucla.edu/html/CoexpressionNetwork/Rpackages/WGCNA/Tutorials/FemaleLiver-Data.zip

Please show a sample of the contents of gsg and datExpr0

ADD REPLYlink modified 11 weeks ago • written 11 weeks ago by Kevin Blighe33k
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1397 users visited in the last hour