WGCNA Eigengene and intramodularConnectivity
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2.2 years ago
AJ ▴ 20

Im trying to get the genes that contribute to the 1st PC, i.e the Eigengene. For this im trying the following function:

https://www.rdocumentation.org/packages/WGCNA/versions/1.68/topics/intramodularConnectivity. There are two ways to execute this function:

1) use of the following syntax:

IntramodularConnectivity(adjMat, colors, scaleByMax = FALSE)


How would I get the adjacency matrix for this function?

2) use of the following syntax:

intramodularConnectivity.fromExpr(datExpr, colors,
corFnc = "cor", corOptions = "use = 'p'",
weights = NULL,
distFnc = "dist", distOptions = "method = 'euclidean'",
networkType = "unsigned", power = if (networkType=="distance") 1 else 6,
scaleByMax = FALSE,
ignoreColors = if (is.numeric(colors)) 0 else "grey",
getWholeNetworkConnectivity = TRUE)


keeps giving me the error:

"Error in intramodularConnectivity.fromExpr(datExpr = datModule_black, : Number of columns (genes) in 'datExpr' and length of 'colors' differ."

wgcna RNA-Seq network • 956 views
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How did you create datExpr and colors? - please confirm that you have followed the WGCNA vignettes / tutorials regarding how to properly create these objects.