Question: Averaging with technical and biological replicates
0
gravatar for Duckula
12 months ago by
Duckula20
Duckula20 wrote:

Dear all,

I have a data-set consisting of biological and technical replicates and I am interested to use the mean expression of them by initially having the mean of the technical replicates and then the biological replicates before analyzing my data-set using DESEQ2. I wonder if any of you have any suggestion that how can I achieve it within R. I am already aware that there is a collapseReplicates in DESEQ2 but it only deals with technical replicates.

The technical and biological replicated would look like something like below

Day-1_1
Day-1_1
Day-1_2
Day-1_2
rna-seq deseq2 next-gen R • 502 views
ADD COMMENTlink modified 12 months ago by zx87548.2k • written 12 months ago by Duckula20
1

Why would you merge your biological replicates ? Good practive is to merge technical replicates only.

ADD REPLYlink written 12 months ago by Nicolas Rosewick8.1k
0
gravatar for Benn
12 months ago by
Benn7.7k
Netherlands
Benn7.7k wrote:

It is not wise to calculate means of technical or biological replicates before doing statistics (the statistical power is in the biological replicates). My advice is to use limma (voom), and use duplicateCorrelation function for the technical replicates.

ADD COMMENTlink modified 12 months ago • written 12 months ago by Benn7.7k
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