Dear Christian

Thank you for your answer and your reactivity.
I have donwloaded the last version of xps but it doesn't work. When I want to load the package I got an error :

> library(xps)
Error in inDL(x, as.logical(local), as.logical(now), ...) : 
  impossible de charger la bibliothèque partagée 'C:/PROGRA~1/R/R-28~1.1/library/xps/libs/xps.dll':
  LoadLibrary failure:  La procédure spécifiée est introuvable.


Erreur : le chargement du package / espace de noms a échoué pour 'xps'

With an error window that say ?GetClass@TClass@@SAPAV1@ABVtype_info@@_N1@Z is not find in libCore.dll. 

Thanks
Best regards

Arnaud

> Date: Sun, 12 Apr 2009 19:42:13 +0200
> From: cstrato@aon.at
> To: arnaudlc@msn.com
> CC: bioconductor@stat.math.ethz.ch; delphine.rossille@chu-rennes.fr
> Subject: Re: [BioC]  Xps package : errors and RMA difference with Partek GS
> 
> Dear Arnaud,
> 
> I have just uploaded a new version xps_1.2.10 (and xps_1.3.12), which 
> corrects the problem with fdr adjustment. Furthermore, I have added 
> option "BY" (see ?uniTest) and crosschecked the results against 
> R-function "p.adjust", thus the results should now be ok.
> 
> Thank you for reporting this problem.
> Best regards
> Christian
> 
> 
> arnaud Le Cavorzin wrote:
> > Dear Christian,
> >
> > Thank you very much for your answer and for your reactivity.
> >
> > We have performed RMA normalization using exonlevel=c(16316,8192,8192) 
> > that is to say using all probes for the background correction and only 
> > metacore probes for the quantile normalization and summarization, so 
> > the same options using by Partek ("core" in Partek corresponding to 
> > "metacore" in xps, like you have suggested it).
> >
> > We get the same number of probeset with Partek and xps package, but 
> > the results are differents for the two softwares.
> > Even if it was better, we found 3539 genes with a p-value<0.05 with 
> > xps, and 3337 genes with p-value<0.05 with Partek, and the results 
> > remain different for the two softwares. We don't obtain the same 
> > p-value, in particular because we don't obtain the same means.
> >
> > I have also imported the data.rma from xps to Partek, and performed 
> > the t test with Partek : the results are the same than performing 
> > unifilter with xps, we obtain the same p value than with xps and the 
> > same means. So they are still different than the results using Partek 
> > only.
> > (Confirm that there is a difference with the probes used in Partek for 
> > the RMA normalization)
> >
> > Another question : when I use fdr correction or no correction with 
> > xps, the results are still the same. Only when I use bonferroni 
> > correction the p-adjusted change. I don't understand why FDR 
> > correction have no effect.
> >
> > /> 
> > unifltr=UniFilter(unitest=c("t.test","two.sided","none",0,0.0,FALSE,0.95,TRUE),
> > + foldchange=c(1,"both"),unifilter=c(0.05,"pval"))
> > > 
> > rma.ufr=unifilter(data.test2.rma,"tmpdt_HuextestUnifilterallmetmet",getwd(),logbase="log2",
> > + unifltr,group=c("075","075","TEM","TEM"),verbose=FALSE)
> > /
> > /> 
> > unifltr=UniFilter(unitest=c("t.test","two.sided","fdr",0,0.0,FALSE,0.95,TRUE),
> > + foldchange=c(1,"both"),unifilter=c(0.05,"pval"))
> > > 
> > rma.ufr=unifilter(data.test2.rma,"tmpdt_HuextestUnifilterallmetmet",getwd(),logbase="log2",
> > + unifltr,group=c("075","075","TEM","TEM"),verbose=FALSE)/
> >
> >
> > Thanks
> > Best regards,
> >
> > Arnaud
> >
> 

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 clics !

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