CGHcall problem
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Erik Dassi ▴ 10
Last seen 8.0 years ago
Hi all, I am trying to analyze my array CGH data for copy number alteration states with CGHcall. My code is as follows: data.CGHcall <- read.table("aCGH_18_log2ratio.txt",header=TRUE,sep='\t', where this table I read in has columns: ProbeName,Chr,Start,End,and then a column for each sample cghRaw <- make_cghRaw(data.CGHcall) cgh <- preprocess(cghRaw,nchrom=22) cgh <- normalize(cgh,method="none") cgh <- segmentData(cgh,method="DNAcopy") cgh <- postsegnormalize(cgh) Everything goes well up to this point, but then I do: cgh <- CGHcall(cgh, prior="auto", nclass=4) [1] "changed" EM algorithm started ... Errore in data.frame(regions2, genord = 1:nreg2) : arguments imply differing number of rows: 0, 2 What kind of error could this be ? Could it be because of some problem of my data ? I checked and after postsegnormalize there are no NAs in the data... so I'm a bit lost.... anyone has had the same problem ? thanks a lot to everybody, Erik -- Erik Dassi PhD Student Laboratory of Translational Genomics CIBIO - Center for Integrative Biology Via delle Regole, 101 38123 MATTARELLO (TN) Italy [[alternative HTML version deleted]]
CGH CGHcall CGH CGHcall • 619 views

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