WGCNA error on block number related.
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yifangt ▴ 20
@yifangt-9770
Last seen 2.7 years ago
Canada/NRC

When I run WGCNA according to tutorial 2.c
I am stuck since this step (2.c.3: comparing single block and block-wise network analysis).
The previous auto- and step-by-step analysis worked fine exactly as the tutorial instructed. Not sure what I missed with this block-wise analysis.

1) #code chunk 5:
plotDendroAndColors(bwnet$dendrograms[[2]], bwModuleColors[bwnet$blockGenes[[2]]],
     "Module colors", main = "Gene dendrogram and module colors in block 2",
     dendroLabels = FALSE, hang = 0.03, addGuide = TRUE, guideHang = 0.05)
# Error in bwnet$blockGenes[[2]] : subscript out of bounds

although it was fine for blockGenes[[1]]

    plotDendroAndColors(bwnet$dendrograms[[1]], bwModuleColors[bwnet$blockGenes[[1]]],
     "Module colors", main = "Gene dendrogram and module colors in block 2",
    dendroLabels = FALSE, hang = 0.03, addGuide = TRUE, guideHang = 0.05)

2) plotDendroAndColors(geneTree, cbind(moduleColors, bwModuleColors, c("Single block", "2 blocks"),      main = "Single block gene dendrogram and module colors",
    dendroLabels = FALSE, hang = 0.03, addGuide = TRUE, guideHang = 0.05)
#  Code chunk 6: Comparing the single block and block-wise network analysis
Error in plotOrderedColors(dendro$order, colors = colors, rowLabels = rowLabels,  :
ERROR: length of colors vector not compatible with number of objects in 'order'.

3) signif(diag(cor(blockwiseMEs[, single2blockwise], singleBlockMEs)), 3)
#  Code chunk 8
Error in `[.data.frame`(blockwiseMEs, , single2blockwise) :  undefined columns selected
bwnet = blockwiseModules(datExpr, (omitted for space))
table(bwLabels)
bwLabels
#   0    1    2    3    4    5    6    7    8    9   10   11   12   13   14   15   16   18   19   22   24   28   30
#1848 1949 1549  912  563  450  535  401  290  417  262   77   58   49   41   50   74   43   37   38   31   36   45

net = blockwiseModules(datExpr, power = 6, ...)
net
......
Block sizes:
gBlocks
   1    2    3
3664 3274 2957

I appreciate any advice on this.
Thanks!

Yifang

WGCNA block size subscript out of bounds • 1.5k views
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It seems like you are mixing objects from the first dendrogram with the second one. But I am unsure if the code you show us is the real one or not

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Thank for the advice!
My code are real fragment. I need more work on my code before I come back soon.

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Hi,

I have problem, exactly, same as you. I appreciate if you share your solution with me.

Best Regards,

Mohammad

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