WGCNA: Why are my brown, yellow, and other modules not visible in the gene dendrogram?

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4 weeks ago

shubhankarpawar3 ▴ 10

I'm conducting a WGCNA analysis on RNA-seq data (total of 24072 genes after gsg). I've obtained a dendrogram that clearly shows two prominent modules, turquoise and blue, containing a majority of the genes. However, brown & yellow modules, which have around 1963 and 1863 genes respectively (similar to the blue module), is barely visible. The WGCNA Parameters are (power=7, networktype= signed, minimum module size=100, merge cut height = 0.25. (note: the module 0 (i.e grey module ) has around 7925 gene out of 24,072 genes). enter image description here

R genes transcriptomics WGCNA • 387 views

ADD COMMENT • link updated 24 days ago by allingt ▴ 40 • written 4 weeks ago by shubhankarpawar3 ▴ 10

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Did you perform blockwise module detection by any chance? Are your results object's contents sorted in blocks?

ADD REPLY • link 24 days ago by allingt ▴ 40

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