[BioC] Input to vsn or limma of genepix file missing 635 columns

Liolios, Konstantinos [BSD] - MED kliolios at medicine.bsd.uchicago.edu
Wed May 14 18:24:27 CEST 2008

Thanx Gordon and Wolfgang,

This worked.


-----Original Message-----
From: Gordon K Smyth [mailto:smyth at wehi.EDU.AU] 
Sent: Saturday, May 10, 2008 11:06 PM
To: bioconductor at stat.math.ethz.ch
Cc: Liolios, Konstantinos [BSD] - MED
Subject: [BioC] Input to vsn or limma of genepix file missing 635

Dear Liolios,

See my post on Bioconductor a few minutes ago titled "Read single
channel Genepix in limma".

Best wishes

> Date: Fri, 9 May 2008 10:52:48 -0500
> From: "Liolios, Konstantinos [BSD] - MED"
> 	<kliolios at medicine.bsd.uchicago.edu>
> Subject: Re: [BioC] Input to vsn or limma of genepix file missing 635
> 	columns
> To: "Wolfgang Huber" <huber at ebi.ac.uk>
> Cc: bioconductor at stat.math.ethz.ch
> Dear Wolfgang,
> Thanx for your reply.  So to make sure:
> 1.  There is no read method in common packages (vsn, marray, affy,
> limma) that can read a single dye genepix file (Cy5/635 related 
> columns
> missing)
> 2.  It is not recommended that I manually add those columns and fill 
> them with 0s or N/A.
> 3.  The best way to proceed is to use vsn2 on a matrix.
> Related to point 2, I actually tried that and was able to use marray 
> read.GenePix which created an marrayRaw object.  It seemed alright but

> I could not reproduce any qc images.  I also could not convert it to 
> an eset using convert even though there is a method that promises such

> a conversion.  Same happened when I created an maNorm object also.
> Finally ?vsn2 did not work on R2.7 and the latest vsn package version.
> I think the default path for the cfm file is incorrect (actually non 
> existent).  However I did manually read the vignette/manual from the 
> library/vsn/html directory.
> Thanx again
> Dinos
> -----Original Message-----
> From: Wolfgang Huber [mailto:huber at ebi.ac.uk]
> Sent: Thursday, May 08, 2008 4:38 AM
> To: Liolios, Konstantinos [BSD] - MED
> Cc: bioconductor at stat.math.ethz.ch
> Subject: Re: [BioC] Input to vsn or limma of genepix file missing 635 
> columns
> Liolios, Konstantinos [BSD] - MED wrote:
>> Dear bioconductors,
>> I have been given Exiqon miRCURY(tm) LNA Array (miRNA) expression gpr

>> files in excel format.  They are single channel so they are actually 
>> missing all 635 related (mean/median/back/for etc.) columns.  I 
>> believe vsn is the way to normalize these data but I can not find 
>> anywhere how to import such a file.  Most tutorials use data that 
>> already come with the package or assume you have .cel files and an 
>> affymetrix annotation file.  I have used read.table which creates a 
>> data.frame but most normalization packages require you to have your 
>> data as an expression set.  I was wondering if somebody knows how to 
>> import single channel gpr files or how to manually create an 
>> expression set from a data.frame w/o an annotation file.
>> Best regards
>> Dinos
> Dear Dinos,
> there is a vsn2 method for "matrix", so please try converting your 
> data.frame into a numeric matrix. Try
> library("vsn")
> ? vsn2
> ? as.matrix
> Also, the vignette "An introduction to Biobase and ExpressionSets", 
> which you can access for example by typing
>  openVignette()
> contains a fairly good set of instructions for making an
> Feedback on possible improvements to the documentation are always 
> welcome.
> Best wishes
>   Wolfgang
> ------------------------------------------------------------------
> Wolfgang Huber  EBI/EMBL  Cambridge UK  http://www.ebi.ac.uk/huber

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