hi everyone,
ive been having problems trying to analyze a group of samples of 250K
using both (Nsp and Sty) enzymes. Ive followed the vignette in
aroma.affymetrix, although i want to use CbsModel instead of
GladModel.
here is some info:
> sessionInfo()
R version 2.11.1 (2010-05-31)
x86_64-pc-mingw32
locale:
[1] LC_COLLATE=Spanish_Spain.1252 LC_CTYPE=Spanish_Spain.1252
[3] LC_MONETARY=Spanish_Spain.1252 LC_NUMERIC=C
[5] LC_TIME=Spanish_Spain.1252
attached base packages:
[1] stats graphics grDevices utils datasets methods
base
other attached packages:
[1] ACNE_0.4.2 NSA_0.0.1
DNAcopy_1.22.1
[4] calmate_0.6.2 MASS_7.3-6
aroma.affymetrix_1.7.0
[7] aroma.apd_0.1.7 affxparser_1.20.0
R.huge_0.2.0
[10] aroma.core_1.7.0 aroma.light_1.16.1
matrixStats_0.2.2
[13] R.rsp_0.4.0 R.cache_0.3.0
R.filesets_0.9.0
[16] digest_0.4.2 R.utils_1.5.3
R.oo_1.7.4
[19] R.methodsS3_1.2.1
here is the code im executing
>setwd("D:/aroma")
>library(aroma.affymetrix)
>library(calmate)
>library(NSA)
>library(ACNE)
>verbose <- Arguments$getVerbose(-8, timestamp=TRUE)
>dataSet <- "CELLungCIMA"
>chipTypes <- c("Mapping250K_Nsp", "Mapping250K_Sty")
>cdfs <- lapply(chipTypes, FUN=function(chipType) {
AffymetrixCdfFile$byChipType(chipType)
})
>gis <- lapply(cdfs, getGenomeInformation)
>sis <- lapply(cdfs, getSnpInformation)
>cesNList <- list()
>chipType <- chipTypes[1]
>cdf <- AffymetrixCdfFile$byChipType(chipType)
>cs <- AffymetrixCelSet$byName(dataSet, cdf=cdf)
>cs <- extract(cs, !isDuplicated(cs))
>acc <- AllelicCrosstalkCalibration(cs, model="CRMAv2")
>csC <- process(acc, verbose=verbose)
>bpn <- BasePositionNormalization(csC, target="zero")
>csN <- process(bpn, verbose=verbose)
>plm <- NmfSnpPlm(csN, mergeStrands=TRUE)
>fit(plm, verbose=verbose)
>ces <- getChipEffectSet(plm)
>fln <- FragmentLengthNormalization(ces)
>cesNList[[chipType]] <- process(fln, verbose=verbose)
and I do the same for the second enzyme with no errors. so finally i
have cesNList which is
> cesNList
$Mapping250K_Nsp
SnpChipEffectSet:
Name: CELLungCIMA
Tags: ACC,-XY,BPN,-XY,NMF,FLN,-XY
Path: plmData/CELLungCIMA,ACC,-XY,BPN,-XY,NMF,FLN,-XY/Mapping250K_Nsp
Platform: Affymetrix
Chip type: Mapping250K_Nsp,monocell
Number of arrays: 105
Names: BN 01 (Mapping250K_Nsp), BN 02 (Mapping250K_Nsp), ..., VB95
(Mapping250K_Nsp)
Time period: 2011-02-07 21:15:39 -- 2011-02-07 21:16:10
Total file size: 1003.43MB
RAM: 0.17MB
Parameters: (probeModel: chr "pm", mergeStrands: logi TRUE)
$Mapping250K_Sty
SnpChipEffectSet:
Name: CELLungCIMA
Tags: ACC,-XY,BPN,-XY,NMF,FLN,-XY
Path: plmData/CELLungCIMA,ACC,-XY,BPN,-XY,NMF,FLN,-XY/Mapping250K_Sty
Platform: Affymetrix
Chip type: Mapping250K_Sty,monocell
Number of arrays: 105
Names: BN 01 (Mapping250K_Sty), BN 02 (Mapping250K_Sty), ..., VB95
(Mapping250K_Sty)
Time period: 2011-02-07 21:20:10 -- 2011-02-07 21:20:36
Total file size: 913.33MB
RAM: 0.17MB
Parameters: (probeModel: chr "pm", mergeStrands: logi TRUE)
but the when i try to do the segmentation it gives an error: (in the
vignette instead of CbsModel, GladModel is used, but I guess if GLAD
works, CBS should do it too)...
> cbs <- CbsModel(cesNList)
Error en UseMethod("as.CopyNumberDataSetTuple") :
no applicable method for 'as.CopyNumberDataSetTuple' applied to an
object of class "c('SnpChipEffectSet', 'ChipEffectSet',
'ParameterCelSet', 'AffymetrixCelSet', 'AffymetrixFileSet',
'AromaPlatformInterface', 'AromaMicroarrayDataSet',
'GenericDataFileSet', 'FullNameInterface', 'Object')"
does anyone knows what might be happening here??
thank you very much,
nice day!
maria
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