DNAcopy package, craeting CNA object
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@jhs1jjmleedsacuk-2338
Last seen 8.4 years ago
Hi, I'm using R 2.5.0 on openSUSE 10.2 x86_64. I'm using some agilent CGH data from 3 arrays. I'm trying to create the CNA object. I've read the agilent data in using the marray package and created the marrayRaw and marrayNorm objects. I'm unsure of what to use for the chromosome and and maploc arguments in the DNAcopy package as follows: Useage: CNA(genomdat, chrom, maploc, data.type=c("logratio","binary"), sampleid=NULL) So far i'm guessing what i'd write would be something like: CNA.object <- CNA(cbind (mraw$maLG,mraw$maRG), chrom, maploc, data.type=c("logratio","binary"), sampleid=NULL) Thanks for any help. John
CGH marray DNAcopy CGH marray DNAcopy • 936 views
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@sean-davis-490
Last seen 5 months ago
United States
jhs1jjm at leeds.ac.uk wrote: > Hi, I'm using R 2.5.0 on openSUSE 10.2 x86_64. > > I'm using some agilent CGH data from 3 arrays. I'm trying to create the CNA > object. I've read the agilent data in using the marray package and created the > marrayRaw and marrayNorm objects. I'm unsure of what to use for the chromosome > and and maploc arguments in the DNAcopy package as follows: > > Useage: > > CNA(genomdat, chrom, maploc, data.type=c("logratio","binary"), > sampleid=NULL) > > So far i'm guessing what i'd write would be something like: > > CNA.object <- CNA(cbind (mraw$maLG,mraw$maRG), chrom, maploc, > data.type=c("logratio","binary"), > sampleid=NULL) You'll need to read the help for CNA(). It explains in some detail what needs to be supplied. In particular, you will need to supply a matrix of ratios for genomedat. Your datatype will be logratio. For chrom and maploc, you will need to determine that for the array that you are using. If you need more guidance, you will probably want to supply the code that you used, the errors that you received when you ran the code, and sessionInfo() when you get the error. Sean

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