Hello, I was wondering if there is any open source software/module available to carry out coexpression analysis of bacterial RNA seq data. I have performed DE seq for differentially expressed genes. I know WGCNA can be adapted but I have only 6 samples (WGCNA requires minimum 20). Can someone give me suggestions?
Hello Kshipra,
It would be best if you could be more specific about your design. What is the number of treatments and how many replicates do you have for each?
WGCNA and co-expression analyses try to separate genes based on correlations, so the more treatments the greater the separation between functional clusters. On the other hand, as Philip points out, if you have insufficient replication per treatment you might mistake random fluctuations in gene expression for coregulation.
You can get an idea of how reliable your differences are from the power-analysis step in your network construction. As a rule of thumb, if your network does not reach a scale-free topology before using a power of 20 it might be best to try another approach, such as principal component analysis or PLS-DA.
Thank you Philip, Jie and Alfredo for your valuable suggestions.
Philip: Can I use Genevestigator if I am working on another gram negative bacteria and not E.coli? I am going through the program for this kind of analysis
Jeil LI: I am not sure, because I have 6 samples (3 strains and 2 treatments) with no replicates but even if I make comparisons within each group, I will end up just 9 comparisons.
Alredo:I have tried the PCA analysis using DEseq and it worked. Thanks!
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