Hi all,

Im using limma for differential expression.

I've been struggling with the concept of my experimental design analysis for a few days so i need some help.

My groups are something like this...

For example, this study is aimed at determining the genes that are responsible for higher Survival rates in dry environments when fed feed2 and feed1+ in comparison to  feed1, using a few different comparison between these 5 treatments.

the easiest method to do this i thought would be to just assign the 5 treatments to a group and then compare the comparisons im interested in.

e.g.

Feed1wet, feed1dry, feed2wet, feed2dry and feed1+dry

My real issue, is that i have been struggling with wether to take Survival into account as a continuous variable.

I thought this made sense at first, but now considering my project aim of determining the genes that may be responsible for survival. I think that i will be masking the DE genes I'm interest in.

e.g. if i want to compare DE genes between feed1dry and feed1+dry to understand why feed1+ has higher survival in dry conditions, accounting for suvival as a continuous variable will mask what im interested in won't it?

what do you think?

thanks

Yes it would.

You could correlate genes directly with survival, but better to do that as a separate analysis without Feed and Condition.