Question: How to compare coexpression networks from two conditions with different sample sizes

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thind.amarinder •

**20**wrote:I have gene expression data from two conditions having different sample sizes i.e 8 and 32. I want to build a correlation among all genes (for both conditions) for comparison. So, I used "psych" package from "R" which use t-test based statistics for p-adjusted values calculations.

Is this approach correct for the comparison of the networks (after taking significant p-adjust) between two experiments of different sample sizes?

or should I use another approach for p-adjusted calculations? If yes, what would you suggest?

Ciao / buonasera, what are you testing with your

psychet-test? I would create the correlation networks separately, and then compare (between the network for each condition) metrics such as vertex degree, hub score, community structure, etc. A simple pipeline, here: Network plot from expression data in R using igraph60kCiao I am not exactly comparing networks. but want to compare interactions of particular set of genes (of my interest) with others (if any), above certain threshold of correlation . whether interacting genes are mostly the same or different in both condition. since sample size is different between conditions, so can I directly compare or not? if, no How I can justify this comparison.

20You want to correlate certain genes in one condition with those in the other condition?

60kYes, how can I go about this?

20You can correlate together where the dimensions are the same, i.e., on the genes. So, probably:

My preferred way would still be to produce a correlation network using all genes and separately for each condition, and then compare your genes based on vertex degree, hub score, and community structure.

60kHow do you calculate significance ( p-adjusted values) for correlation?

20There is a

`cor.test()`

function, which functions in the same way as the`cor()`

function. After you derive your p-values, you can then adjust for false discovery with`p.adjust()`

60kThank you, it seems the way "psych" calculated p.adjust is similar.

20