Question: Unequal number of technical and biological replicates per sample for RNA-Seq expriment?
0
gravatar for gaelgarcia
4.3 years ago by
gaelgarcia150
UK
gaelgarcia150 wrote:

Hi,

I performed an RNAseq experiment for two conditions, with 4 biological replicates for Condition 1 and 2 biological replicates for Condition 2.

Furthermore, I have three technical replicates for 2 of the biological replicates in Condition 1, and no technical replicates for the other two biological replicates of Condition 1 (only one instance of each). 

For Condition 2, biological replicate 1 had two technical replicates, while biological replicate 2 had three technical replicates.

 

Will this un-evenness in replicates (both technical and biological) affect the downstream analysis?

I am using DESeq2 and collapsing technical replicates by adding the raw counts into a single sample, as explained in the DESeq manual.

Any input is appreciated. Thank you.

 

 

sequencing rna-seq deseq deseq2 R • 2.8k views
ADD COMMENTlink modified 4.3 years ago by Irsan7.0k • written 4.3 years ago by gaelgarcia150
1
gravatar for alolex
4.3 years ago by
alolex900
United States
alolex900 wrote:

First I want to say I am not a biostatistician, so please consult a biostatistician for details about the statistics of your particular situation.  With that said, you should always determine the number of replicates and the statistical tests you are going to use BEFORE you run the experiment.  This should be part of the experimental design process so that you can ensure you have enough replicates to get the power you need to detect changes.  However, sometimes things go wrong and you get shorted data.  I'm not sure what happened here, so I am assuming this is all you have to work with.  

Yes, you should always combine technical replicates.  I don't think the unevenness will cause problems, but the lack of replicates will.  Generally I prefer 3 or more.  Having only 2 biological replicates in one condition may adversely affect your power to detect real changes.  Please consult with a biostatistician on this if you plan to publish using only 2 replicates for one condition; otherwise I think it is ok for exploratory analysis to see if anything really big jumps out at you.  Others may have different thoughts and I emplor them to chime in here.        

ADD COMMENTlink written 4.3 years ago by alolex900
0
gravatar for Irsan
4.3 years ago by
Irsan7.0k
Amsterdam
Irsan7.0k wrote:
In your situation you should use something that implements mixed-effects modeling beause you have both technical and biological replicates. Try for example ShrinkBayes. I wouldnt care too much about Power analyses because you have to make a dozen of assumptions and most of the time the study is limited by money and sample availability anyway. It can be very helpful though to contact a bio-informatician/statistician before starting your experiments for many other reasons. I would have told you to forget about the technical replicates.
ADD COMMENTlink modified 4.3 years ago • written 4.3 years ago by Irsan7.0k
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1719 users visited in the last hour