Do or not doing the Co-expression data analysis?
I have 2 genotypes of Sorghum and got samples from upper and basal parts of stem. I have RNA-seq data for 3 biological data. I'm just wondering that can I do co-expression data analysis or for co-expression data analysis I need to have time-series data or more different conditions?
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My bigger concern will be the sample size. At least for WGCNA, it requires around minimum of 12 samples per condition for any reasonable co-expression network to be constructed.
I see, at the most I have3 samples per condition (3 sections of stems considered as the condition and 2 or 3 genotypes as the sample), therefore you don't recommend that?
@Sam is taking about the specific Bioconductor package here "WGCNA", which requires atleast 12 samoles to perform co-expression analysis. You could do the co-expression analysis, but would not be able to say much about expression, because, samples size matters. Have a look through this link: Any Tutorial For Co-Expression(Network) Analysis?
I have 3 biological replicates.
Check this: Minimum Number Of Samples (Biological Replicates) Required For Co -Expression Network Analysis