Question: RNA-seq analysis design
gravatar for illinois.ks
12 months ago by
Korea, Republic Of
illinois.ks160 wrote:

Dear all,

I am analysing our RNA-seq data to find DEG responding our drug combinations and have a few questions.

I have 4 conditions and per each condition I have 3 replicates

group 1. Control (3 replicates)
group 2. Disease model (3 replicates)
group 3. Disease model + 1 drugs ( 3 replicates) 
group 4. Disease model + 1 drugs + 1 adjuvants  ( 3 replicates)

My hypothesis is that the drug is effective, and hopefully with adjuvants, it is much more effective....

In order to test this hypothesis I would like to compare several things.

comparison 1.  group 1 vs group 2 ( the genes affected by disease) 
comparison 2. group 2 vs group 3 (the genes affected by drug ) 
comparison 3. group 3 vs group 4 (the genes affected by adjurvants)  
comparison(maybe) 4. group 1 vs group 3 (expect that there are not so many DEG if drug is effective) 
comparison (maybe) 5. group 1 vs group 4 (expect that there are not so many DEG if drug+adjurvants is effective)

First of all, I made a dataset with these 4 groups of data to find DEGs responding one of above comparions. (by adjusting other factors)

However, it seems that it brings too many variances due to the group 2 (which is a disease model ) Note that other three groups indicate the cure model ( recovered from disease)

Could you please someone recommend that whether I just need to compare only each of two groups? ( For example, for comparison 1 , I can just use two data set from group 1 and group2 etc.. )

rna-seq • 379 views
ADD COMMENTlink modified 12 months ago by Devon Ryan94k • written 12 months ago by illinois.ks160
gravatar for Devon Ryan
12 months ago by
Devon Ryan94k
Freiburg, Germany
Devon Ryan94k wrote:

You're usually better off fitting all of the groups at once (a design like ~group) and using contrasts for the various comparisons, since you get the best variance fit. That is, don't subset the data for each comparison, just fit the whole thing.

ADD COMMENTlink written 12 months ago by Devon Ryan94k
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