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8.1 years ago

mahnazkiani
▴
50

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?

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