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...
| Feed | condition | survival |
| feed1 | wet | 10 |
| feed1 | wet | 4 |
| feed1 | wet | 6 |
| feed1 | wet | 4 |
| feed1 | dry | 3 |
| feed1 | dry | 3 |
| feed1 | dry | 4 |
| feed1 | dry | 5 |
| feed2 | wet | 10 |
| feed2 | wet | 8 |
| feed2 | wet | 5 |
| feed2 | wet | 7 |
| feed2 | dry | 9 |
| feed2 | dry | 5 |
| feed2 | dry | 6 |
| feed2 | dry | 8 |
| feed1+ | dry | 9 |
| feed1+ | dry | 5 |
| feed1+ | dry | 8 |
| feed1+ | dry | 7 |
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
