Hi all,
I was using EdgeR to perform a DE analysis and following the document http://cgrlucb.wikispaces.com/file/v...R_Tutorial.pdf.
Essentially edgeR tutorial.pdf.
I did an exact test on my samples using cmn, tgw and poi.
de.poi <- exactTest( cds , dispersion = 1e-06 , pair = c( "Control" , "Infected" ) )
I have also created a toptags table for all three, cmn , tgw and poi.
> resultsTbl.cmn <- topTags( de.cmn , n = nrow( de.cmn$table ) )$table
> resultsTbl.tgw <- topTags( de.tgw , n = nrow( de.tgw$table ) )$table
> resultsTbl.poi <- topTags( de.poi , n = nrow( de.poi$table ) )$table
Here is my question or rather questions:
1. My exact test values for cmn and tgw are exactly the same !!!!! I plotted a variance plot and the
plot for cmn (solid blue line) and tgw (lt.blue dots) are exactly on each other (as if superimposed). So I believe I dont have a tagwise dispersion. Anyone has had this experience???
2. when I try to perform a significance level matching to 0.05 I get nothing !!!
> de.genes.cmn <- rownames( resultsTbl.cmn )[ resultsTbl.cmn$adj.P.Val <= 0.05 ]
> de.genes.tgw <- rownames( resultsTbl.tgw )[ resultsTbl.tgw$adj.P.Val <= 0.05 ]
> de.genes.poi <- rownames( resultsTbl.poi )[ resultsTbl.poi$adj.P.Val <= 0.05 ]
> head(de.genes.cmn)
character(0)
> de.genes.cmn
character(0)
### I do have values in my resultsTbl, see below !!!!! Also you can see how my resultsTbl values for cmn and tgw are exactly the same !! as discussed in Q1.
> head(resultsTbl.cmn)
logFC logCPM PValue FDR
ENSBTAG00000029982 5.80 7.59 5.66e-11 1.30e-08
ENSBTAG00000036418 7.88 5.63 1.56e-06 1.78e-04
ENSBTAG00000036410 1.34 16.34 7.29e-06 5.57e-04
ENSBTAG00000036423 2.29 10.97 7.59e-05 4.34e-03
ENSBTAG00000029762 1.68 10.61 2.66e-04 1.22e-02
ENSBTAG00000037319 -1.92 4.41 3.48e-04 1.33e-02
> de.genes.tgw
character(0)
> head(resultsTbl.tgw)
logFC logCPM PValue FDR
ENSBTAG00000029982 5.80 7.59 5.66e-11 1.30e-08
ENSBTAG00000036418 7.88 5.63 1.56e-06 1.78e-04
ENSBTAG00000036410 1.34 16.34 7.29e-06 5.57e-04
ENSBTAG00000036423 2.29 10.97 7.59e-05 4.34e-03
ENSBTAG00000029762 1.68 10.61 2.66e-04 1.22e-02
ENSBTAG00000037319 -1.92 4.41 3.48e-04 1.33e-02
> head(resultsTbl.poi)
logFC logCPM PValue FDR
ENSBTAG00000036423 1.9671 11.0 0 0
ENSBTAG00000029957 1.1314 15.6 0 0
ENSBTAG00000036410 1.1289 16.3 0 0
ENSBTAG00000029797 0.7093 15.7 0 0
ENSBTAG00000029897 0.3867 15.5 0 0
ENSBTAG00000029804 0.0894 18.3 0 0
Can anyone throw some light on this please?
Much appreciated,
geneart.
I was using EdgeR to perform a DE analysis and following the document http://cgrlucb.wikispaces.com/file/v...R_Tutorial.pdf.
Essentially edgeR tutorial.pdf.
I did an exact test on my samples using cmn, tgw and poi.
de.poi <- exactTest( cds , dispersion = 1e-06 , pair = c( "Control" , "Infected" ) )
I have also created a toptags table for all three, cmn , tgw and poi.
> resultsTbl.cmn <- topTags( de.cmn , n = nrow( de.cmn$table ) )$table
> resultsTbl.tgw <- topTags( de.tgw , n = nrow( de.tgw$table ) )$table
> resultsTbl.poi <- topTags( de.poi , n = nrow( de.poi$table ) )$table
Here is my question or rather questions:
1. My exact test values for cmn and tgw are exactly the same !!!!! I plotted a variance plot and the
plot for cmn (solid blue line) and tgw (lt.blue dots) are exactly on each other (as if superimposed). So I believe I dont have a tagwise dispersion. Anyone has had this experience???
2. when I try to perform a significance level matching to 0.05 I get nothing !!!
> de.genes.cmn <- rownames( resultsTbl.cmn )[ resultsTbl.cmn$adj.P.Val <= 0.05 ]
> de.genes.tgw <- rownames( resultsTbl.tgw )[ resultsTbl.tgw$adj.P.Val <= 0.05 ]
> de.genes.poi <- rownames( resultsTbl.poi )[ resultsTbl.poi$adj.P.Val <= 0.05 ]
> head(de.genes.cmn)
character(0)
> de.genes.cmn
character(0)
### I do have values in my resultsTbl, see below !!!!! Also you can see how my resultsTbl values for cmn and tgw are exactly the same !! as discussed in Q1.
> head(resultsTbl.cmn)
logFC logCPM PValue FDR
ENSBTAG00000029982 5.80 7.59 5.66e-11 1.30e-08
ENSBTAG00000036418 7.88 5.63 1.56e-06 1.78e-04
ENSBTAG00000036410 1.34 16.34 7.29e-06 5.57e-04
ENSBTAG00000036423 2.29 10.97 7.59e-05 4.34e-03
ENSBTAG00000029762 1.68 10.61 2.66e-04 1.22e-02
ENSBTAG00000037319 -1.92 4.41 3.48e-04 1.33e-02
> de.genes.tgw
character(0)
> head(resultsTbl.tgw)
logFC logCPM PValue FDR
ENSBTAG00000029982 5.80 7.59 5.66e-11 1.30e-08
ENSBTAG00000036418 7.88 5.63 1.56e-06 1.78e-04
ENSBTAG00000036410 1.34 16.34 7.29e-06 5.57e-04
ENSBTAG00000036423 2.29 10.97 7.59e-05 4.34e-03
ENSBTAG00000029762 1.68 10.61 2.66e-04 1.22e-02
ENSBTAG00000037319 -1.92 4.41 3.48e-04 1.33e-02
> head(resultsTbl.poi)
logFC logCPM PValue FDR
ENSBTAG00000036423 1.9671 11.0 0 0
ENSBTAG00000029957 1.1314 15.6 0 0
ENSBTAG00000036410 1.1289 16.3 0 0
ENSBTAG00000029797 0.7093 15.7 0 0
ENSBTAG00000029897 0.3867 15.5 0 0
ENSBTAG00000029804 0.0894 18.3 0 0
Can anyone throw some light on this please?
Much appreciated,
geneart.
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