[BioC] support for miRNA-1_0?

[Dick Beyer]

Hi Christian,

Thanks very much for the update on xps.  I'll give it a try and let you know how it works.

Cheers,
Dick
*******************************************************************************
Richard P. Beyer, Ph.D.	University of Washington
Tel.:(206) 616 7378	Env. & Occ. Health Sci. , Box 354695
Fax: (206) 685 4696	4225 Roosevelt Way NE, # 100
 			Seattle, WA 98105-6099
http://depts.washington.edu/ceeh/ServiceCores/FC5/FC5.html
http://staff.washington.edu/~dbeyer
*******************************************************************************

On Wed, 12 Aug 2009, cstrato wrote:

> Dear Dick,
>
> Some weeks ago I have updated package xps to allow some support of the miRNA 
> aray, and have uploaded "xps_1.5.13" to the BioC development branch.
>
> Here is the code to create the scheme and import the CEL-files:
>
> # import scheme:
> # note: you need to rename "miRNA-1_0.probe_list.20081203.txt" to 
> "miRNA-1_0.probe.tab"
> libdir <- "/Volumes/GigaDrive/Affy/libraryfiles"
> scmdir <- "/Volumes/GigaDrive/CRAN/Workspaces/Schemes"
> scheme.mirna <- import.expr.scheme("Scheme_miRNA_1_0",filedir=scmdir,
>               paste(libdir,"miRNA-1_0.CDF",sep="/"),
>               paste(libdir,"miRNA-1_0.probe.tab",sep="/"))
>
> # import CEL-files (test files from Affymetrix)
> datdir <- getwd()
> celdir <- "/Volumes/GigaDrive/ChipData/miRNA/genisphere_affymetrix_dataset"
> celnames <- c("BrainTotal", "LiverLMW", "LiverTotal")
> data.mirna <- 
> import.data(scheme.mirna,"DatamiRNA",filedir=datdir,celdir=celdir,celnames=celnames)
>
> As you see, you need to rename the probe file and you cannot use the special 
> Affymetrix annotation file since it does not follow the standard annotation 
> layout.
>
>
> In a new R session you can load the scheme and data files as usual, and do RMA:
>
> # load scheme and data
> scmdir <- "/Volumes/GigaDrive/CRAN/Workspaces/Schemes"
> datdir <- getwd()
> scheme.mirna <- root.scheme(paste(scmdir,"Scheme_miRNA_1_0.root",sep="/"))
> data.mirna <- root.data(scheme.mirna, 
> paste(datdir,"DatamiRNA_cel.root",sep="/"))
>
> # RMA
> data.rma <- 
> rma(data.mirna,"miRNA_RMA",tmpdir="",background="pmonly",normalize=T)
>
> # get expression level data.frames
> expr.rma <- validData(data.rma)
> head(expr.rma)
>
>
> You can also do some visualization:
>
> # for raw data you need to attach data first
> data.mirna <- attachMask(data.mirna)
> data.mirna <- attachInten(data.mirna)
>
> # plots
> image(data.mirna)
> hist(data.mirna)
> boxplot(data.mirna)
> hist(data.rma)
> boxplot(data.rma)
>
> Please note that currently all probesets for all different organisms are used 
> for RMA.
>
> Since I have no access to miRNA data, I would be interested in reports from 
> users trying xps for miRNA, especially if RMA normalization gives reasonable 
> results.
>
> 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
> _._._._._._._._._._._._._._._._._._
>
>
> Dick Beyer wrote:
>> Are there any plans to support the new affy microRNA chip: miRNA-1_0?
>> 
>> Thanks,
>> Dick
>> 
>> ******************************************************************************* 
>> Richard P. Beyer, Ph.D.    University of Washington
>> Tel.:(206) 616 7378    Env. & Occ. Health Sci. , Box 354695
>> Fax: (206) 685 4696    4225 Roosevelt Way NE, # 100
>>             Seattle, WA 98105-6099
>> http://depts.washington.edu/ceeh/ServiceCores/FC5/FC5.html
>> http://staff.washington.edu/~dbeyer
>> 
>> _______________________________________________
>> Bioconductor mailing list
>> Bioconductor at stat.math.ethz.ch
>> https://stat.ethz.ch/mailman/listinfo/bioconductor
>> Search the archives: 
>> http://news.gmane.org/gmane.science.biology.informatics.conductor
>> 
>> 
>
>