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
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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