Re: error in WGCNA

[pankaj]

Basically you are using the >keepSamples = (clust==1) step extra in your case as in yur case> table(clust)  results

clust

 0 

14 

Something is wrong with your input matrix 'datExpr'. Check

 >dim(datExpr)

If you are happy with the sample clustering, and no obvious outlier detected, then go with >datExpr<-datExpr0  instead of datExpr = datExpr0[keepSamples, ]

---

Pankaj

On Monday, March 4, 2013 12:16:13 PM UTC+1, Paulami Chatterjee wrote:

During WGCNA while calculating connectivity for given powers I am having the following error -

Error in { : task 1 failed - "'x' has a zero dimension."

I have given the following codes. Can anyone help me solving this problem please?

> sampleTree = flashClust(dist(datExpr0), method = "average");

> sizeGrWindow(12,9)

> par(cex = 0.6);

> par(mar = c(0,4,2,0))

> plot(sampleTree, main = "Sample clustering to detect outliers", sub="", xlab="", cex.lab = 1.5,

+ cex.axis = 1.5, cex.main = 2)

> clust = cutreeStatic(sampleTree, cutHeight = 40, minSize = 35)

> table(clust)

clust

 0 

14 

> keepSamples = (clust==1)

> datExpr = datExpr0[keepSamples, ]

> nGenes = ncol(datExpr)

> nSamples = nrow(datExpr)

> powers = c(c(1:10), seq(from = 12, to=20, by=2))

> sft = pickSoftThreshold(datExpr, powerVector = powers, verbose = 5)

pickSoftThreshold: will use block size 2205.

 pickSoftThreshold: calculating connectivity for given powers...

   ..working on genes 1 through 2205 of  2205

Error in { : task 1 failed - "'x' has a zero dimension."

In addition: Warning message:

executing %dopar% sequentially: no parallel backend registered 

[genome medicine]

Hi Pankaji:

I have samples with normal and tumors, after I get the color modules, how can i do the epigengene associate with specific moduals, It is hard to follow the tuturol. Thanks,

William

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