Hi, everyone,
I am new in WGCNA. I have two RNA-seq data sets collected from two different developmental stages of maize endosperm (developmental stages can be considered as "interesting" condition). Both data sets have same format with GeneID at first column, and FPKM values for samples at rest columns.The sequencing and processing procedures are similar except that the first data set is "2X50-nucleotide paired-end reads" and the second is "2X100-nucleotide paired-end reads". Also, the variation between two data sets are very large, like the first is around 5~500-fold greater than the second. My concern is whether I could combine them together to run WGCNA? or whether I need to do some adjustments before I take any action? If yes, could you give me some suggestions about how to adjust the data in order to make it valid for WGCNA. Thanks in advance.
