Question: RNA-seq analysis design
0
gravatar for illinois.ks
6 weeks ago by
illinois.ks140
Korea, Republic Of
illinois.ks140 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 • 163 views
ADD COMMENTlink modified 6 weeks ago by Devon Ryan90k • written 6 weeks ago by illinois.ks140
4
gravatar for Devon Ryan
6 weeks ago by
Devon Ryan90k
Freiburg, Germany
Devon Ryan90k 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 6 weeks ago by Devon Ryan90k
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