Entering edit mode
4.0 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."
How did you create
datExpr
andcolors
? - please confirm that you have followed the WGCNA vignettes / tutorials regarding how to properly create these objects.