Re: [aroma.affymetrix] calmate error (doASCRMAv2)

2013-01-04 Thread Siyuan Zheng
; > > dataSet <- 'mydata' > > chipType <- "GenomeWideSNP_6" > > cdf <- AffymetrixCdfFile$byChipType(chipType, tags="Full") > > csR <- AffymetrixCelSet$byName(dataSet, cdf=cdf) > > dsList <- doASCRMAv2(csR, plm="RmaCnPlm",

Re: [aroma.affymetrix] calmate error (doASCRMAv2)

2013-01-04 Thread Henrik Bengtsson
le$byChipType(chipType, tags="Full") > csR <- AffymetrixCelSet$byName(dataSet, cdf=cdf) > dsList <- doASCRMAv2(csR, plm="RmaCnPlm", verbose=verbose) > cmt <- CalMaTeCalibration(dsList); > dsCList <- process(cmt, verbose=verbose); > > Error message: >

Re: [aroma.affymetrix] calmate error (doASCRMAv2)

2013-01-04 Thread Zheng Siyuan
<- doASCRMAv2(csR, plm="RmaCnPlm", verbose=verbose) cmt <- CalMaTeCalibration(dsList); dsCList <- process(cmt, verbose=verbose); Error message: 20130104 16:48:19|CalMaTe calibration of ASCNs... 20130104 16:48:19| Number of arrays: 6 20130104 16:48:19| Number of references: 6 201

Re: [aroma.affymetrix] calmate error (doASCRMAv2)

2013-01-04 Thread Zheng Siyuan
df <- AffymetrixCdfFile$byChipType(chipType, tags="Full") > > csR <- AffymetrixCelSet$byName(dataSet, cdf=cdf) > > #print(csR) > > dsList <- doASCRMAv2(csR, plm="RmaCnPlm", verbose=verbose) > > #print(dsList) > > > > Error message is > >

Re: [aroma.affymetrix] calmate error (doASCRMAv2)

2013-01-04 Thread Henrik Bengtsson
eSNP_6" > cdf <- AffymetrixCdfFile$byChipType(chipType, tags="Full") > csR <- AffymetrixCelSet$byName(dataSet, cdf=cdf) > #print(csR) > dsList <- doASCRMAv2(csR, plm="RmaCnPlm", verbose=verbose) > #print(dsList) > > Error message is > > ... &g

Re: [aroma.affymetrix] Errors when processed Vignette:CRMAv2

2013-01-04 Thread Foxchase
NetAffx > files. > > I use a public data 'GSE27691". Attached is the R history file. > > When I followed the Vignette:CRMAv2 I got error at the step:> cesN <- > > process(fln, verbose=verbose): > > > >> cesN <- process(fln, verbose=verbose)

[aroma.affymetrix] calmate error (doASCRMAv2)

2013-01-04 Thread Zheng Siyuan
uot;RmaCnPlm", verbose=verbose) #print(dsList) Error message is ... 20130104 14:42:50| Fitting...done 20130104 14:42:50| Allele probe-pair group #7 ('missing') of 7...done 20130104 14:42:50| Fitting calibration model...done *Error in UseMethod("sapply&qu

Re: [aroma.affymetrix] Errors when processed Vignette:CRMAv2

2013-01-04 Thread Pierre Neuvial
se=verbose): > >> cesN <- process(fln, verbose=verbose) > 20130104 12:05:43|Normalizing set for PCR fragment-length effects... > 20130104 12:05:44| Identifying SNP and CN units... > types > 1 2 5 >24 626135 1832538 > 20130104 12:05:44| subset

Re: [aroma.affymetrix] unexpected result form Paired total copy-number analysis

2013-01-04 Thread Saman Amini
Great, yes it helped! Thanks, Saman On Thursday, 3 January 2013 11:09:32 UTC-6, Henrik Bengtsson wrote: > > Hi. > > On Thu, Jan 3, 2013 at 12:11 AM, Saman Amini > > > wrote: > > > > Hi all, > > > > I am using aroma.affymetrix to get the segmented paired copy numbers for > raw CELL files a

[aroma.affymetrix] Errors when processed Vignette:CRMAv2

2013-01-04 Thread Foxchase
I got error at the step:> cesN <- process(fln, verbose=verbose): > cesN <- process(fln, verbose=verbose) 20130104 12:05:43|Normalizing set for PCR fragment-length effects... 20130104 12:05:44| Identifying SNP and CN units... types 1 2 5 24 626135 1