WGCNA out of memory
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Entering edit mode
zli1 • 0
@cd41d80f
Last seen 7 weeks ago
United States

Hi,

I'm trying to use WGCNA to analyze a large RNA seq data (~60000 genes). Currently, I am using the codes

blockwiseModules(t(nCount), maxBlockSize = nrow(nCount),power = 5,
                       TOMType = "signed", minModuleSize = 30,
                       reassignThreshold = 0.7, mergeCutHeight = 0.25,
                       numericLabels = TRUE, pamRespectsDendro = FALSE,
                       saveTOMs = TRUE,
                       saveTOMFileBase = "RNATOM", 
                       verbose = 3)

When running on a workstation with ~130 G memory, I received a failure message "out of memory". I am setting maxBlockSize = nrow(nCount) to avoid pre-clustering of genes, but this seems to give rise to this issue. What would be a recommended parameter?

Thank you!

wgcna RNASeq • 82 views
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