Soft threshold in WGCNA

Question

[madkitty]

Hi,

I get that error message when following the tutorial to determine the soft threshold. We have 3 dataset as controls(datExpr1, datExpr2, datExpr3) and 1 dataset containing 10 replicates (datExpr4).

I tried to limit the analysis to common genes between the 3 datasets controls and the replicates with the following lines:

commonGenes1 = intersect (rownames(datExpr1),rownames(datExpr4))
commonGenes2 = intersect (rownames(datExpr2),rownames(datExpr4))
commonGenes3 = intersect (rownames(datExpr3),rownames(datExpr4))

datExpr1= datExpr1[commonGenes1,]
datExpr2= datExpr2[commonGenes2,]
datExpr3= datExpr3[commonGenes3,]

Then we have to find the "soft threshold" .. and that's where I got the error message, it seems that it needs too much memory. I'm suspecting I'm doing smth wrong when calling the common set of genes between the 3 datasets controls and the samples..

# Choose a set of soft-thresholding powers
powers = c(c(1:10), seq(from = 12, to=20, by=2))

# Call the network topology analysis function
sft = pickSoftThreshold(samExpr0, powerVector = powers, verbose = 5)
pickSoftThreshold: will use block size 29382.
pickSoftThreshold: calculating connectivity for given powers...
   ..working on genes 1 through 29382 of 34688
Error in { : task 2 failed - "cannot allocate vector of size 1.9 Gb"
In addition: There were 12 warnings (use warnings() to see them)

[Devon Ryan]

You're probably running out of memory. As a general rule of thumb, any time you ever see a message like "cannot allocate vector of size ..." then that's what's happening.