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

[Liolios, Konstantinos [BSD] - MED]

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 ExpressionSet. 
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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