Hi, My RNA-seq data set belongs to TCGA data bank. I download this data set by TCGAbiolinks package.for using this package, I define a special query that one argument of this query is workflow.type = "HTSeq - FPKM-UQ". I mean, my data is Normal. So, for using this data as WGCNA input, I transform it to log2 value. But, in bioconductor support froum, I see some below comment from the author of model:
"you can certainly use WGCNA for RNA-seq data. Two recommendations: 1. Filter out genes whose count is less than say 5 in more than say 80% of the samples. This gets rid of a lot of noise and gets rid of expression profiles for which correlation makes little sense. 2. Use a variance-stabilizing transformation, such as the one implemented in varianceStabilizingTransformation or rlogTransformation in the DESeq2. I have analyzed a few RNA-seq data sets and have had great results."
Now, I don't know my data set needs any additional pre-processing or not? I appreciate if anybody share his/her comment with me. Best regards, Mohammad