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Old 08-22-2012, 02:21 PM   #1
carmeyeii
Senior Member
 
Location: Mexico

Join Date: Mar 2011
Posts: 137
Default How to find elements in group comparison A but not B in EdgeR?

Hi everyone!

I am running edgeR to find the set of genes differentially expressed in a variety of genotypes. I think I have the list of differentially expressed genes for each genotype compared to the control, but do not understand how I can obtain ONLY the ones diff. expressed in situation 1 but not situation 2 (my controls). The data type of these tables seems to be a "package" so I can-t figure out how to use the function setdiff() between my list elements 1 and to and between 3 and 4.

Anyone else had to do this before?

Thanks a lot,

Carmen

> differentialExp = list(diffOverExpVSCtrl, diffLacZCtrlVSCtrl, diffMutantVSCtrl, diffRescueVSCtrl)

> differentialExp

I wish to have a table with the genes differentially expressed in this table but not the one below:
[[1]]
Comparison of groups: 2-1
PValue
w 9.338566e-18
Cyp4p2 4.096677e-14
snoRNA:Me18S-A425 5.101414e-14
CG14608 4.033759e-11
Cyp4p1 8.742902e-11
Myo28B1 1.019588e-10
CG8245 1.065524e-09
CG6912 7.234873e-09
CG3984 2.704771e-08
CG6299 8.302330e-08

[[2]]
Comparison of groups: 2-1
PValue
w 2.694068e-30
CR40507 3.478277e-19
CG8245 1.395445e-18
CG14608 3.767024e-15
Dbi 3.814363e-13
CG6299 4.025586e-13
CR40508 9.007926e-13
CR40528.4 3.109278e-12
Su(Ste):CR42413.1 6.150114e-11
Su(Ste):CR42413 2.232705e-10


And also I wish to have a table with the genes differentially expressed in this table but not the one below:

[[3]]
Comparison of groups: 2-1
PValue
CG31663 7.918141e-10
ImpL3 1.437678e-09
Su(Ste):CR42441.1 2.262814e-08
Dbi 3.990401e-08
snoRNA:Me28S-C3227b 4.756527e-08
CG9743 6.102312e-08
snoRNA:Me28S-G3113b 7.640097e-08
CG10226 7.674893e-08
snmRNA:357 1.014492e-07
Hsp70Aa.1 1.082010e-07

[[4]]
Comparison of groups: 2-1
PValue
CG17352 7.216395e-17
CG9380 1.899326e-15
CR40507 2.703574e-12
snmRNA:763 1.216682e-11
CR31808 1.464365e-11
ImpL3 2.321142e-11
MED9 8.672577e-11
snoRNA:Me18S-A425 1.131187e-10
Nep2 2.419856e-09
snoRNA:Psi18S-1377b 2.679469e-09


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Old 08-26-2012, 11:47 PM   #2
Gordon Smyth
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Location: Melbourne, Australia

Join Date: Apr 2011
Posts: 91
Default

Finding overlaps between DE lists is easy in edgeR, and doesn't require setdiff().

But you don't explain how you created the data objects diffOverExpVSCtrl and so on, so it is hard to give any help. Are they perhaps output from topTags()?

Gordon
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