Question: compare rna seq samples with different replications
1
gravatar for filipa.tome
4.7 years ago by
Germany
filipa.tome0 wrote:

Hi,

I have data from a RNAseq experiment, where different genotypes and treatments were tested. I am analyzing the data using edgeR (fit <- glmFit(dgeObj, design) ).

The design is as follows, where a, b, c and d are the different factors for the comparison, and 1-8 are the samples. So sample 1,2 and 3 are biological replicates, and so are 5,6, and 7. Factors b and d only have 1 biological replicate.

> design <- data.frame(a=c(1,1,1,0,0,0,0,0), b=c(0,0,0,1,0,0,0,0), c=c(0,0,0,0,1,1,1,0), d=c(0,0,0,0,0,0,0,1))

> design

  a b c d

1 1 0 0 0

2 1 0 0 0

3 1 0 0 0

4 0 1 0 0

5 0 0 1 0

6 0 0 1 0

7 0 0 1 0

8 0 0 0 1

 

This is the contrast I want to make:

 

> contrast <- makeContrasts(a - b - (c - d), levels=colnames(design))
> contrast
      Contrasts
Levels (a - b) - (c - d)
     a               1
     b              -1
     c              -1
     d               1

 

So I want to compare samples that have 3 biological replicates to samples that only have 1. Is this possible?

I don’t understand how edgeR gives statistics for the coefficient of interest despite the lack of replicates (how was variance estimated there?). What are your thoughts on this?

Thanks!

 

replication rna-seq • 1.4k views
ADD COMMENTlink written 4.7 years ago by filipa.tome0
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: 1211 users visited in the last hour