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Erik Dassi
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10
@erik-dassi-4043
Last seen 10.2 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',as.is=TRUE)
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
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