[BioC] problem with siggenes

[Fangxin Hong]

First, please ignore the emails I sent out yesterday, I was using an old
version of siggenes.

However, I do find problems with siggenes. There is Excel version SAM
method which can be downloaded from Stanford website. For the same data
set, I got very different results from siggenes and from Excel SAM,

> out=sam(data,cl,delta=seq(0.1,7,0.1),rand=123)
> FDR=summary(out)[,5]
> Delta=summary(out)[,1]
> d.min=min(Delta[FDR<0.05])
> gene.list1=summary(out,d.min,ll=FALSE)$row.sig.genes
> gene.list2=list.siggenes(out,d.min)

siggenes identify much less genes than Excel SAM does. In addition, if
only one gene identified using certain delta value,
summary()$row.sig.genes (gene.list1 above) will not list that gene since
there is error in the function. list.siggenes will only print the
identified genes out, but won't assign gene list/name to other object
(gene.list2 is empty in the example)

Anyone knows what is going on here or what mistakes I might made.

Thanks.
Fangxin

> As far as I know, if you only have two arrays, one from each "treatment"
> in your experiment, there is no way that you can do any kind of statistics
> at all....
>
> -----Original Message-----
> From: bioconductor-bounces at stat.math.ethz.ch
> [mailto:bioconductor-bounces at stat.math.ethz.ch] On Behalf Of Edoardo
> Saccenti
> Sent: 13 January 2005 16:45
> To: bioconductor at stat.math.ethz.ch
> Subject: [BioC] problem with siggenes
>
>
> I would like to manage a FDR analysis via
> SAM as implemented in siggenes package.
>
> First I read 2 file.CEL into an affybatch object called "mydata" Then i
> used rma routine to correct my data obtaining an exprSet object called
> "myeset"
>
> According to the guide I need to pass to sam
> the data (myeset in this case) and a vector cl
>
> This is a one class case,  so
> so cl must be a vector of ones of length equal to number
> of sample.
> As the number of sample is 2 (2 CEL files)
>
> cl <- c(1,1)
>
> Typing at the R prompt:
>
> 	out <- sam.dstat(myeset, cl, rand=123)
>
> I get the following:
>
> 	We're doing 4 complete permutations
> 	Error in rowSums(x, prod(dn), p, na.rm) : invalid value of n
> 	In addition: Warning message:
> 	There are 147 genes with zero variance. These genes are removed,
> 	and their d-values are set to NA.
>
> I'm sure I'm doing some stupid mistake 'couse I'm new to R and BioC:
> nevertheless can anybody help me?
>
> Thanks
> edoardo
>
>
>
> "Raffiniert ist der Herr Gott,
>  aber boshaft ist Er nicht."
>
> ---
> Dr. Edoardo Saccenti
> FiorGen Pharmacogenomics Foundation
> CERM Nuclear Magnetic Resonace Research Center
> Scientific Pole - University of Florence
> Via Luigi Sacconi n° 6
> 50019 Sesto Fiorentino (FI)
> tel: +39 055 4574193
> fax: +39 055 4574253
> saccenti at cerm.unifi.it
> www.cerm.unifi.it
>
> _______________________________________________
> Bioconductor mailing list
> Bioconductor at stat.math.ethz.ch
> https://stat.ethz.ch/mailman/listinfo/bioconductor
>
> _______________________________________________
> Bioconductor mailing list
> Bioconductor at stat.math.ethz.ch
> https://stat.ethz.ch/mailman/listinfo/bioconductor
>
>


-- 
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