From GEO to aCGH and snapCGH
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João Fadista ▴ 500
@joao-fadista-1942
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@sean-davis-490
Last seen 12 weeks ago
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Jo?o Fadista wrote: > Hi, > > Does anyone knows how can I convert the format from a GEO (Gene Expression Omnibus) CGH dataset to a format suitable to be analysed by the snapCGH and aCGH packages? > Joao, What is the GEO accession number? Does the platform information include a chromosome and location for the probes? What have you tried and what hasn't worked? Sean
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@sean-davis-490
Last seen 12 weeks ago
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Jo?o Fadista wrote: > Hi, > > Thanks for the tip. > I already have the chromosome and the position of the gene entrez ids. Do you know how can I substitute in my MAList the MA$genes$Entrez.GeneID with both the columns Position and Chr? > That's great. You can use the merge() function to join the MA$genes data frame with the data frame that contains the Entrez Gene ID and associated Position and Chromosome. Sean
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@sean-davis-490
Last seen 12 weeks ago
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Jo?o Fadista wrote: > Dear Sean Davis, > > I already put the Position and Chromosome elements in the $genes dataframe. > So then I tried again the function processCGH, but it gave me this error: > > >> MA5 <- processCGH(MA4, method.of.averaging = mean, ID="ID") >> > Processing chromosome 1 > Processing chromosome 10 > Processing chromosome 11 > Processing chromosome 12 > Processing chromosome 13 > Processing chromosome 14 > Processing chromosome 15 > Processing chromosome 16 > Processing chromosome 17 > Processing chromosome 18 > Processing chromosome 19 > Processing chromosome 2 > Processing chromosome 20 > Processing chromosome 21 > Processing chromosome 22 > Error in if (kb >= chrominfo$centromere[chr]) median(vec[clones.info$Chr == : > missing value where TRUE/FALSE needed > > Do you have any idea of what could be wrong? Thanks again for helping me. > > It appears that you are making progress, Joao. Just for future reference, when you reply to messages from an email list, it is best to reply to the list so that everyone can learn from the discussion and so that you get the best advice possible. In this case, I'm not sure what is causing your error, but others on the list likely do know what the problem is and most likely have a solution for you. Sean > -----Original Message----- > From: Sean Davis [mailto:sdavis2 at mail.nih.gov] > Sent: 26 November 2006 02:41 > To: Jo?o Fadista; bioconductor at stat.math.ethz.ch > Subject: Re: [BioC] From GEO to aCGH and snapCGH > > Jo?o Fadista wrote: > >> Hi, >> >> Thanks for the tip. >> I already have the chromosome and the position of the gene entrez ids. Do you know how can I substitute in my MAList the MA$genes$Entrez.GeneID with both the columns Position and Chr? >> >> > > That's great. You can use the merge() function to join the MA$genes data frame with the data frame that contains the Entrez Gene ID and associated Position and Chromosome. > > Sean >
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