wgcna module preseravtion taking too long?
0
0
Entering edit mode
lamia11me • 0
@121cda19
Last seen 14 hours ago
United States

how long does WGCNA module preservation takes? I have two datasets, 10 sampels each, 9800 genes each. using a 32GB windows with multithreading (10 cores). It's been running for hours now.

```

make list

multiExpr <- list(A = list(data = b6expr), B = list(data = s1expr))

multiColor <- list(A = b6colors)

Run mod preserve

mp <- modulePreservation(multiExpr, multiColor, referenceNetworks = 1, # use strain A as reference networkType = "unsigned", nPermutations = 1, maxGoldModuleSize = 100, maxModuleSize=400, verbose = 3)

sessionInfo( )

```..checking data for excessive amounts of missing data.. Flagging genes and samples with too many missing values... ..step 1 Flagging genes and samples with too many missing values... ..step 1 ..unassigned 'module' name: grey ..all network sample 'module' name: gold ..calculating observed preservation values ..calculating permutation Z scores ..Working with set 1 as reference set ....working with set 2 as test set ......working on permutation 1

WGCNA • 23 views
ADD COMMENT

Login before adding your answer.

Traffic: 2299 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6