Question: CGHcall problem
gravatar for Erik Dassi
9.2 years ago by
Erik Dassi10
Erik Dassi10 wrote:
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 • 449 views
ADD COMMENTlink written 9.2 years ago by Erik Dassi10
Please log in to add an answer.


Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 16.09
Traffic: 141 users visited in the last hour