EdgeR without replicate?
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3.2 years ago

I am doing DEG analysis between two sample (Normal vs Treated) without replicates using edgeR. I know there is no significance of analysis without replicates, but i have no other choice.

library(edgeR)
bcv <- 0.2

counts <- data
y <- DGEList(counts=counts, group=1:2)
et <- exactTest(y, dispersion=bcv^2)


The count matrix was generated by Corset, which gives the count matrix in Poisson distribution while i am applying exactTest which takes count matrix as negative binomial distribution. Should i carry on with this analysis only or use another test equivalent to exactTest for Poisson distributed count matrix? If there is any other test then what it is? What value of dispersion should be taken according to the data-set?

my variable:

>y

An object of class "DGEList"
$counts Normal.bam Treated.bam Cluster-0.0 0 50 Cluster-1.0 0 25 Cluster-2.0 0 16 Cluster-2.1 0 8 Cluster-3.0 0 15 ... more rows ...$samples         group     lib.size      norm.factors
Normal.bam      1          3.22e+07              1
Treated.bam     2          1.05e+08              1

>et

An object of class "DGEExact"
$table logFC logCPM PValue Cluster-0.0 8.03 -1.58 4.06e-05 Cluster-1.0 7.04 -2.39 2.13e-03 Cluster-2.0 6.40 -2.89 3.49e-02 Cluster-2.1 5.42 -3.58 7.51e-02 Cluster-3.0 6.31 -2.95 3.49e-02 202654 more rows ...$comparison
[1] "1" "2"

\$genes
NULL

RNA-Seq edgeR Corset differential' • 5.5k views
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For Gordon Smyth's expert answer see: https://support.bioconductor.org/p/124721/