Question: RNA seq query
0
gravatar for komal
9 months ago by
komal0
komal0 wrote:

Hello Everyone, I did RNA seq of 1 normal and 1 treated sample. I used STAR for alignment (GRCh38.p12 genome), featurecount for abundance calculation and deseq2 for differential analysis. when i used deseq2 for transcript wise differential analysis i got proper up and down regulated genes but when i used deseq2 for gene wise differential analysis i didn't got up and down regulated genes. can you tell me what will be the reason for this??

rna-seq • 207 views
ADD COMMENTlink written 9 months ago by komal0
4
gravatar for WouterDeCoster
9 months ago by
Belgium
WouterDeCoster44k wrote:

I did RNA seq of 1 normal and 1 treated sample.

An analysis without replicates is statistically invalid.

ADD COMMENTlink written 9 months ago by WouterDeCoster44k

For more information please google (and use the internal search function) for differential analysis without replicates. There are literally dozens of posts, blogs, manuals that discuss that topic.

ADD REPLYlink written 9 months ago by ATpoint38k

Thanks for your reply. I will try that.

ADD REPLYlink modified 9 months ago • written 9 months ago by komal0

An analysis without replicates is statistically invalid.

It's true but that data is already sequences so i don't have any option.

ADD REPLYlink modified 9 months ago • written 9 months ago by komal0
1

There is no computational method that will magically render an underpowered experiment to be well-powered. Your experimental design is flawed as 1 vs 1 is not statistically solid. Nothing you can do about it, sorry. Best you can do is some exploratory analysis. Please read previous posts on how to do this, as this has been discussed many times before.

ADD REPLYlink written 9 months ago by ATpoint38k
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