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WGCNA maxBlockSize limit

Recently I ran a WGCNA network construction analysis. The array type has more than 50K genes but luckily I have a powerful cluster which has more than 600G memory, so I set the maxBlockSize=60000. But I got the error message: 'maxBlockSize must be less than 46340. Please decrease it and try again.' Where does this 46340 come frome? Can I use any size of maxBlockSize if I have enough memory? Thank you. -Xiaokuan

wgcna
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written by weixiaokuan weixiaokuan

How much memory is on the current Node you are using? The tutorial says "32GB workstation should handle perhaps 30000." Are you multi-threading the WGCNA analysis?

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written by informatics bot informatics bot

At first I did enable multi-thread for WGCNA. After I found this error, I disabled multi-threading but this error still exists. -Xiaokuan

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written by weixiaokuan weixiaokuan

You didn't answer my question. How much memory is on the node you're using?

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written by informatics bot informatics bot

it has about 600G memory on the node I was using.

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written by weixiaokuan weixiaokuan

I think you should/could use a variance filter to remove non-variant genes before doing network construction.

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written by WouterDeCoster WouterDeCoster

I want to use all the genes not filtered ones. I guess that's one of the feature of WGCNA, it will identify eigengenes from matrix and no need to filter. my point is that i have large memory available but it seems I cannot take advantage of it. -Xiaokuan

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written by weixiaokuan weixiaokuan

I don't agree, genes with (nearly) no expression might show spurious correlation just by having small counts...

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written by WouterDeCoster WouterDeCoster

I believe OP is using micro-array data not RNAseq

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written by informatics bot informatics bot

yes, I used microarray.

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written by weixiaokuan weixiaokuan

Answer by Peter Longfelder from bioconductor fourm:

"The limit is (the square root of) the maximum matrix size addressable by a 4-byte pointer. I will eventually update the WGCNA code to remove the limit, but for now it is what it is. The limit is independent of how much memory you have. Sorry! Peter

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written by weixiaokuan weixiaokuan

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