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shresthavivek18
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@shresthavivek18-22711
Last seen 4.9 years ago
Hello, I did a WGCNA analysis on around ~ 4000 genes with 30 samples. WGCNA created 5 gene modules based on their coexpression but I found that there are numbers of genes (ranges from 1- 40) that overlap with one or other modules. Is this overlapping of genes between two modules are Ok? If not what might be the issue and how can I solve this? Please let me know. Thank you
Could you please post the code you used? It will make it easier to suggest changes to avoid this. Also 4000 genes seems like a low number, did you filter the genes before using WGCNA?
Here is the code, (also the original data had ~8000 genes, after filtering the poor quality it has around ~4000). Thank you
zmnet = blockwiseModules(zmdatExpr, power = 18,corType = "pearson", TOMType = "signed", minModuleSize = 30, reassignThreshold = 0, mergeCutHeight = 0.25, numericLabels = TRUE, pamRespectsDendro = FALSE, saveTOMs = TRUE, saveTOMFileBase = "B73maizepower18TOM2", verbose = 3)
It is strange that you needed such a high power. Could you show more code?
for soft threshold power, https://drive.google.com/open?id=1ZyZlRWW0O9s7F0YaLJIxeHzVXKN7MiKV Let me know if you have any comments? Shoud I have stick to B=12?
I did not know any simple code to extract genes within each modules, so did this,
zmmodules_overlap <- overlapTableUsingKME( zmdatExpr, zmdatExpr, moduleColors, moduleColors, MEs1 = NULL, MEs2 = NULL, name1 = "MM1", name2 = "MM2", cutoffMethod = "assigned", cutoff = 0.5, omitGrey = TRUE, datIsExpression = TRUE)
genesMM1 <- zmmodulesoverlap$GenesMM1
and then manually extract the genes in each modules. Is there any simple code after module construction to extract genes within each modules?
For a "signed" network, power 18 is not exceptionally high. Especially for lower numbers of samples (below say 30) it may be entirely appropriate.
Ok great, thank you! I think I figured out there were some problems during the filtration process where I did not remove all of the duplicated genes. Thank you Lluis and Peter for taking the time to answer my question. I appreciate your help. However, still if you know any code that can directly generate/extract the gene list within each module; that would be great! Thanks a lot.