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

Wolfgang Huber huber at ebi.ac.uk
Thu May 8 11:38:27 CEST 2008

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

? vsn2
? as.matrix

Also, the vignette "An introduction to Biobase and ExpressionSets", 
which you can access for example by typing


contains a fairly good set of instructions for making an ExpressionSet. 
Feedback on possible improvements to the documentation are always welcome.

Best wishes

Wolfgang Huber  EBI/EMBL  Cambridge UK  http://www.ebi.ac.uk/huber

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