Question: Minimum number of replicates for gene co-expression analysis
1
gravatar for 4galaxy77
3.6 years ago by
4galaxy7760
United Kingdom
4galaxy7760 wrote:

Hi,

I am looking to see if there is a difference in the number and membership of gene co-expression networks between two different treatments (from RNAseq data). I was going to use WGCNA but I have too few replicates (14/15 compared to the 20 they suggest) for it to work reliably.

Generally is 14/15 replicates too few for any analysis, or are there other programs which would be able to use this number?

Thanks

rna-seq gene expression • 2.1k views
ADD COMMENTlink modified 2.5 years ago by Manoj0 • written 3.6 years ago by 4galaxy7760

They suggest 20 but they say minimum is 15. It also depends on how good are these replicates in terms of variation.

ADD REPLYlink written 3.6 years ago by geek_y10k

Just give it a try with your samples. As Goutham Atla wrote, it depends on how strong the variation is between your replicates. If there rather similar, 15 is probably fine. If they're very different, you might want 50 ;)

ADD REPLYlink written 3.6 years ago by WouterDeCoster43k
0
gravatar for Manoj
2.5 years ago by
Manoj0
Manoj0 wrote:

WGCNA is not recommended when sample size is less than 15 WGCNA

You can try getting the correlation coefficient (pearson correlation, etc ) between the genes based on their expression across conditions and construct a network based on a  threshold(say 0.9).

ADD COMMENTlink modified 2.5 years ago • written 2.5 years ago by Manoj0
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