Dear All, I performed an RNA seq experiment comparing virus-infected animals vs control animals. The goal is to see how these two animal groups would differ in gene expression. I realized that infected animals were of 13 male + 11 female and in the control animals: 15 male , 16 female. As you know sex chromosome could have genes that bias the analyses. How can I test if this gender variation between the two groups could bias the analyses, so could shift somehow the expression of some gene towards one sex. I performed chi-square to test association and it was non significant. Any ideas
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mohsamir2016 •
1 answer
You could run an initial analysis without accounting for the sex (e.g. ~condition), and look at how your samples split based on few PCs.
If there is a clear difference between the two groups, then you need to account for that variability like cpad0112 suggested (e.g. ~Sex + condition).
In the figure above, the samples are not splitting by sex, so it should be safe to avoid the correction.
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if you have used DESeq2/EdgeR, include sex in model (~ condition+sex). If other variables in experiment are influenced by sex, include interaction in the model.
Thanks for the answers. I already created an nMDS. Here I run 3 nMDS:
How do you think is the sepration. I run Permanova to test significant differences among groups (see P-value above the figure). Now which is these figures are best answering the question ? Beacuse I assume looking into each group (e.g. within infected). if male and female seprated then there is a sex bias inside this group, meaning that infection did affects gene expression in a sex-dependent manner ? am I right
I also though about logistic regression analyses as a statitical approach to test this ? how do you think ?
use DESeq2/EdgeR as suggested and get back to us if you need help