[BioC] 2 sample t test using xps package

Tue Mar 10 21:04:41 CET 2009

Dear Christian:
Thanks for the help to my previous question. So far I have gone through
all normalization and filtering steps and ready to do the t test. When I
did the normalization, I use all 30 exon array files, but for the t
test, I would like to leave some files out, in this case, is there a way
to code this information in the "unifilter" function "group = " option
without rerun the script again? Another minor question is about
"PreFilter" lothreshold and hithreshold options. Even though I have read
the manual of the package, I still have trouble of understanding the
detailed definition (or calculation) of these two cutoff. Would you
please give me a lit bit more explanations.

Thanks again

Best regards

Yonghong 

-----Original Message-----
From: cstrato [mailto:cstrato at aon.at] 
Sent: Monday, March 09, 2009 4:56 PM
To: Wang, Yonghong (NIH/NCI) [C]; bioconductor at stat.math.ethz.ch
Subject: Re: [BioC] Package "xps" import.data error

Dear Yonghong

First, please reply always to the list, too. This will allow others to 
search the mailing list.

The error message you get means that your CEL-files must be pretty old, 
since they contain in the header part "DatHeader=" of the CEL-files the 
chip type "HuEx-1_0-st-v1.1sq".

The suggestion to change the name of HuEx-1_0-st-v2 to HuEx-1_0-st-v1 is

one possibility.

Another possibility is to change the header of the CEL-files as 
Affymetrix did, see:
http://www.affymetrix.com/analysis/netaffx/exon/announcements.affx
"changed the chiptype setting in the CEL files from HuEx-1_0-st-v1 to 
HuEx-1_0-st-v2"

The above link also explains why it would be a bad idea to use the 
original HuEx-1_0-st-v1.pgf file for further analysis.

Best regards
Christian

Wang, Yonghong (NIH/NCI) [C] wrote:
>
> Dear Christian:
>
> Thanks for your quick response. According to your suggestions, I 
> reinstalled the newest version of xps package and reran the code under

> the "RTerm" and got the following error message:
>
> *Opening file 
> <c:/R_file/CRAN/Workspaces/Schemes/Scheme_HuEx10stv2r2_na27f.root> in 
> <READ> mode...*
>
> *Creating new file <c:/R_file/ROOTData/test_data_cel.root>...*
>
> *Importing <c:/R_file/CEL/H2452.CEL> as <H2452.cel>...*
>
> *Error: Selected scheme <HuEx-1_0-st-v2> is not identical to imported 
> scheme <HuEx-1_0-st-v1>.*
>
> *Error: Selected scheme <c:/R_file/CEL/H2452.CEL> is not identical to 
> imported scheme <>.*
>
> *Error in import.data(scheme.exon, "test_data", filedir = datdir, 
> celdir = celdir, :*
>
> * error in function 'ImportData'*
>
> Search Rmailing list, one suggestion is to change the name of 
> HuEx-1_0-st-v2 to HuEx-1_0-st-v1 (since I could not find the cdf of 
> HuEx-1_0-st-v1. In my case, I use the following code to generate the 
> Root.scheme:
>
> *scheme.huex10stv2r2.na27e <- 
> import.exon.scheme("Scheme_HuEx10stv2r2_na27e",filedir=scmdir,*
>
> * layoutfile=paste(libdir,"HuEx-1_0-st-v1.r1.clf",sep="/"),*
>
> * schemefile=paste(libdir,"HuEx-1_0-st-v1.r1.pgf",sep="/"),*
>
> *
probeset=paste(anndir,"HuEx-1_0-st-v2.na27.hg18.probeset.csv",sep="/"),*
>
> * 
>
transcript=paste(anndir,"HuEx-1_0-st-v2.na27.hg18.transcript.csv",sep="/
"))*
>
> In which I simply change the name of "HuEx-1_0-st-v2.r2.clf" to 
> "HuEx-1_0-st-v1.r1.clf", and "HuEx-1_0-st-v2.r2.pgf" to 
> "HuEx-1_0-st-v1.r1.pgf", without changing the actual content of clf 
> and pfg file. So far it works. My questions (or concerns) are whether 
> these kinds of changes are valid, and whether these changes affect the

> final annotation result?
>
> Thanks for the help
>
> Best regards
>
> Yonghong
>
> -----Original Message-----
> From: cstrato [mailto:cstrato at aon.at]
> Sent: Monday, March 09, 2009 3:03 PM
> To: Wang, Yonghong (NIH/NCI) [C]
> Cc: bioconductor at stat.math.ethz.ch
> Subject: Re: [BioC] Package "xps" import.data error
>
> Dear Yonghong
>
> Since you are using xps with Windows I suppose that you are using
RGui.
>
> In order to get more information about your problem may I suggest to
run
>
> xps using RTerm with verbose=TRUE. This will show you more information
>
> and give you a hint about the concrete problem, see:
>
>
https://www.stat.math.ethz.ch/pipermail/bioconductor/2008-December/02545
2.html
>
> Could you please send me the complete output from RTerm.
>
> Could you also please update to a newer version of xps, xps_1.0.2 is
>
> pretty old.
>
> Maybe, one last note: From your code I assume that you have imported
the
>
> exon scheme in the same R session as the CEL-files. Since the pgf and
>
> annotation files consume huge amounts of memory it is better to import
>
> the exon scheme in a separate R session first. When starting a new R
>
> session you can use "root.scheme()" to import the created scheme and
>
> import the CEL-files in the new R session.
>
> Please let me know if this could solve your problem, otherwise please
>
> send me the output from RTerm, as already mentioned.
>
> Best regards
>
> Christian
>
> _._._._._._._._._._._._._._._._._._
>
> C.h.r.i.s.t.i.a.n S.t.r.a.t.o.w.a
>
> V.i.e.n.n.a A.u.s.t.r.i.a
>
> e.m.a.i.l: cstrato at aon.at
>
> _._._._._._._._._._._._._._._._._._
>
> Wang, Yonghong (NIH/NCI) [C] wrote:
>
> > Hello all:
>
> >
>
> > I am new to XPS package and would like to use it to perform
affymetrix
>
> > EXON array data analysis. Basically I copied and paseted the sample
>
> > codes and ran the analysis. Originally, I tried some test dataset
(cel
>
> > files) and works fine. But when I ran my cel files, I got the error
>
> > message. Basically I can't import the Cel files into R package. The
code
>
> > I was using is listed below. I am using window system with R version
>
> > 2.8.1. I am thinking that the error might be caused by some kinds of
>
> > incompatibilities, but can't prove it. Any helps would be very
>
> > appreciated.
>
> >
>
> > Best
>
> >
>
> > Yonghong
>
> >
>
> >
>
> >
>
> > Code:
>
> >
>
> >
>
> >
>
> >
>
> >> setwd("c:/R_file")
>
> >>
>
> >
>
> >
>
> >> library(xps)
>
> >>
>
> >
>
> >
>
> >
>
> > Welcome to xps version 1.0.2
>
> >
>
> > an R wrapper for XPS - eXpression Profiling System
>
> >
>
> > (c) Copyright 2001-2008 by Christian Stratowa
>
> >
>
> >
>
> >
>
> >
>
> >> homedir <- "c:/R_file/"
>
> >>
>
> >
>
> >
>
> >> libdir <- paste(homedir, "libraryfiles", sep="")
>
> >>
>
> >
>
> >
>
> >> anndir <- paste(homedir, "Annotation", sep="")
>
> >>
>
> >
>
> >
>
> >> scmdir <- paste(homedir, "CRAN/Workspaces/Schemes", sep="")
>
> >>
>
> >
>
> >
>
> >> celdir <- paste(homedir, "CEL", sep="")
>
> >>
>
> >
>
> >
>
> >> datdir <- paste(homedir, "ROOTData", sep="")
>
> >>
>
> >
>
> >
>
> >> tmpdir <- paste(homedir, "CRAN/Workspaces/Exon/temp", sep="")
>
> >>
>
> >
>
> >
>
> >> celfiles <- c("H2452.CEL", "H2596.CEL")
>
> >>
>
> >
>
> >
>
> >> celnames <- substring(celfiles,1)
>
> >>
>
> >
>
> >
>
> >> scheme.huex10stv2r2.na27f <-
>
> >>
>
> > import.exon.scheme("Scheme_HuEx10stv2r2_na27f",filedir=scmdir,
>
> >
>
> > +
>
> > layoutfile=paste(libdir,"HuEx-1_0-st-v2.r2.clf",sep="/"),
>
> >
>
> > +
>
> > schemefile=paste(libdir,"HuEx-1_0-st-v2.r2.pgf",sep="/"),
>
> >
>
> > +
>
> >
probeset=paste(anndir,"HuEx-1_0-st-v2.na27.hg18.probeset.csv",sep="/"),
>
> >
>
> > +
>
> >
transcript=paste(anndir,"HuEx-1_0-st-v2.na27.hg18.transcript.csv",sep="/
>
> > "))
>
> >
>
> >
>
> >> scheme.exon
>
> >>
>
> >
<-root.scheme(paste(scmdir,"Scheme_HuEx10stv2r2_na27f.root",sep="/"))
>
> >
>
> >
>
> >> test.data<- import.data(scheme.exon, "test_data",filedir = datdir,
>
> >>
>
> > celdir = celdir, celfiles = celfiles, verbose = FALSE)
>
> >
>
> > Error in import.data(scheme.exon, "test_data", filedir = datdir,
celdir
>
> > = celdir, :
>
> >
>
> > error in function 'ImportData'
>
> >
>
> >
>
> >
>
> >
>
> > [[alternative HTML version deleted]]
>
> >
>
> > _______________________________________________
>
> > Bioconductor mailing list
>
> > Bioconductor at stat.math.ethz.ch
>
> > https://stat.ethz.ch/mailman/listinfo/bioconductor
>
> > Search the archives: 
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>
> >
>
> >
>
> >
>