Entering edit mode
Dear Liolios,
See my post on Bioconductor a few minutes ago titled "Read single
channel
Genepix in limma".
Best wishes
Gordon
> 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
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
