EdgeR without replicate?
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Entering edit mode
2.2 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)
data = read.table("MYFILE-counts.txt", header=T, row.names=1, com='')
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' • 3.7k views
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Entering edit mode

For Gordon Smyth's expert answer see: https://support.bioconductor.org/p/124721/

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