I have a bulk RNAseq dataset with 24 samples under 4 groups/conditions. I would like
Group/Condition1 : With tumor and treated with a drug (T-D-P1 and T-D-P2)(two populations each with three replicates)
Group/Condition2 : With tumor and no treatment (T-S-P1 and T-S-P2)(two populations each with three replicates)
Group/Condition3 : No tumor but treated with a drug (WT-D-P1 and WT-D-P2)(two conditions each with three replicates)
Group/Condition4 : No tumor and No treatment (WT-P1 and WT-P2)(two conditions each with three replicates)
We are interested in normalizing the effect of drug. I am therefore looking for a way to somehow "subtract" the known gene expression signature of between T-D-P1 and WT-D-P1 and similarly for T-D-P2 and WT-D-P2.
Then I am interested in comparing
- the normalized (T-D-P1 minus WT-D-P1) versus T-P1
- the normalized (T-D-P2 minus WT-D-P2) versus T-P2
- (normalized (T-D-P1 minus WT-D-P1) versus T-P1) versus normalized (T-D-P2 minus WT-D-P2) versus T-P2
Please consider validating your past questions by upvoting comments/accepting answers. This is an appropriate way to show appreciation for the help that you receive here.
First I posted this question and then I checked my previous query. Sorry genomax you people are really great in sparing your valuable time and helping us with our queries.
Unless original posters accept answers it becomes difficult to judge if answers provided actually helped solve the problem (mods can accept answers but we prefer not to do that since that is best done by person who asked the original question). This also gives future visitors to the forum confidence that the answer is correct.
You have many past questions that have answers that fall in this category. Would be great if you could accept valid answers (green check mark) when you find some time.
Yes, in some of the posts, I didn't accept the answers. I thought it didn't completely address my query. Hereafter in future I will make sure of it. Thanks genomax.
You could add a note to that effect (what was not addressed). Information future visitors would find useful. You don't have to accept the answer if it does not do what you needed to a large extent.
Sure, I will update myposts.