[R] [BioC] How to analysis Y98 chips using RankProd package?

[fhong@salk.edu]

> Dear R and Bioconductor Helpers,
>
> I am using a package called RankProd under Bioconductor to analysis my
> Y98 (yeast) microarray data. I had no problem following the example in
> the vignette but got stocked when I tried to analyze my own data.
>
> When I tried to run the following command,
>
> RP.out <- RP(rrf.sub, rrf.cl.sub, gene.names = y98.gnames, rand = 123)
>
> I got the following response:
>
> Rank Product analysis for two-class case
>
> Starting 100 permutations...
> Computing pfp ..
> Error in "row.names<-.data.frame"(`*tmp*`, value = c("logical(0)",
> "logical(0)",  :
>         duplicate 'row.names' are not allowed
I would guess that your gene name y98.gnames has duplicates, meaning one
gene name appears more than once.  This is normal since genes might be
spotted more than once on one chip, I think I would change my program to
accomodate this. But for now, it would be fine if you can change your gene
name to avoid duplicates. I will let you know when after I checked my
program.

Fangxin



> What is the problem? Is there something wrong with my gene names file?
> How can I fix it?
>
> Thank you very much for your kind help.
>
>
> Best Regards,
>
> - Cleo
>
>
>
> Chia-Wen Cleo Chang
> PhD Student
> CMB, BioCentrum-DTU, Building 223, room 213
> Technical University of Denmark, DK-2800 Lyngby, Denmark
> Telephone: +45 4525 2997, Fax: +45 4588 4148
> E-mail: cwc at biocentrum.dtu.dk
>
>
>
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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