Hello Guys,
I'm using the package RankProduct to determine the differential expression of
genes in 2 classes.
The importance of the thing is to know:
- How can I determine which class is the class of up-regulated
genes and which to the down regulated gene
- How can i interpret the results :
$pfp, $RPs, $RPrank,
Orirank,
$Orirank$"class1 > class 2"
$Orirank$"class1 < class 2"
$AveFC
Table1: Genes called significant under class1 < class2
Table2: Genes called significant under class1 > class2
Thanks for your help.
Example:
Formula:
RP.out<-RP(data, pt.cl, g.names, num.perm = 100, logged = TRUE,
na.rm = FALSE, plot = FALSE, rand =123)
$pfp
class1 < class2 class1 > class 2
1 0.97115385 0.002000000
$RPs
class1 < class2 class1 > class 2
1 37.54242 21.63239
$RPrank
class1 < class2 class1 > class 2
1 26.0 5.0
Orirank
$Orirank$"class1 < class2"
[,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,10] [,11] [,12]
..
$Orirank$"class1 > class 2"
..
$AveFC
log/unlog(class1/class2)
1 0.0694052288
#Genes by controlling pfp <0.05
!
topGene(RP.out, cutoff = 0.05, logged = TRUE, logbase = 2, g.names)
Table1: Genes called significant under class1 < class2
Table2: Genes called significant under class1 > class2
$Table1
gene.index RP/Rsum FC:(class1/class2) pfp
Gen n 51 15.8595 0.8204 0.0000
Gen n-1 65 18.3764 0.9582 0.0250
Gen n-2 75 18.6893 0.8916 0.0167
Gen n-3 52 19.0778 0.8928 0.0150
.
$Table2
gene.index RP/Rsum FC:(class1/class2) pfp
Gen n-3 98 10.0913 1.4331 0.0000
Gen n-2 39 15.2657 1.4062 0.0000
Gen n-1 2 19.8796 1.1414 0.0000
Gen n 97 20.3225 1.1446 0.0000
...
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