EdgeR without replicate?
Entering edit mode
4.6 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.

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:


An object of class "DGEList"
                     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


    An object of class "DGEExact"
            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 ...

[1] "1" "2"

RNA-Seq edgeR Corset differential' • 7.4k views
Entering edit mode

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


Login before adding your answer.

Traffic: 1138 users visited in the last hour
Help About
Access RSS

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6