Input to vsn or limma of genepix file missing 635 columns
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@gordon-smyth
Last seen 57 minutes ago
WEHI, Melbourne, Australia
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
Annotation Normalization Biobase affy vsn limma marray convert Annotation Normalization • 695 views
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@liolios-konstantinos-bsd-med-2786
Last seen 8.4 years ago
Thanx Gordon and Wolfgang, This worked. Dinos -----Original Message----- From: Gordon K Smyth [mailto:smyth@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 columns 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 This email is intended only for the use of the individua...{{dropped:8}}

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