[BioC] Rank Product

[fhong@salk.edu]

Hi Nadine,

> 1. I tried to calculate the Rank product in Excell (as explain in the
> paper
> of Rainer Breitling) using a small data set,  i didn't get the same
> results
> as calculating it with R-Programm.
> Can somebody help me?
The RankProd package under bioconductor is programmed according to the
original paper by Rainer, which means the results should be similar if you
program it in excel according to the paper too. You might observe small
difference which is due to different random number generator used in Excel
and in R.


> 2. How can i understand the results obtaining from Rankproduct
> for example:
> class1 = c(rep(0,40))
> class2 =c( rep(1, 24))
>
> cl<-c(rep(0,40), rep(1,24))
> Table 1 class1<class2: Is that the up-regulated genes in classs1 compare
> to
> class 2?
> Table 2: class1>class2: Is that the down-regulated genes in class1 compare
> to class2?
The two tables are explained in package vignette, I will double check to
make sure that it is up to date.
Since it is class1<class2, table 1 lists genes that are up-regulated in
class2 compared with class 1. And table 2(class1> class2) lists genes that
are down-regulated in class 2 compared with class 1.
>
> 3. How does R-Programm calculates the RP/Rsum?
If you call RP or RPadvance, the output is RP;if you call RSadvance, it is
Rsum. For RP, it is programmed according to the original paper. For Rsum,
instead of getting produce of rank, it compute the average rank.

Hopefully this helps.
fangxin


> Thanks for your help
>
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--------------------
Fangxin Hong  Ph.D.
Plant Biology Laboratory
The Salk Institute
10010 N. Torrey Pines Rd.
La Jolla, CA 92037
E-mail: fhong at salk.edu
(Phone): 858-453-4100 ext 1105