Entering edit mode
Manisha Brahmachary
▴
80
@manisha-brahmachary-2692
Last seen 10.2 years ago
Hello,
If anybody in this forum uses the aroma affymetrix, I will be very
obliged
if you can help me with this query:
I am doing an unpaired copy number analysis with 500K arrays using the
CRMAv2. I want to use a subset of my samples the reference, instead of
the all the samples as robust average for CBS segmentation. So I want
to run CBS as CbsModel(ref,tumor). I am stuck at the point where I
cannot extract the subset of samples for reference properly. Since the
CnChipEffectSet is a list of two enzyme set, how do I extract out the
subset of samples for both enzymes
I have also listed the error I get below:
Here is the code I run:
library(aroma.affymetrix)
log <- Arguments$getVerbose(-4, timestamp=TRUE)
dataSetName<- "Test"
chipTypes <- c("Mapping250K_Nsp","Mapping250K_Sty")
cdfs <- lapply(chipTypes, FUN=function(chipType) {
AffymetrixCdfFile$byChipType(chipType)
})
print(cdfs)
gis <- lapply(cdfs, getGenomeInformation)
print(gis)
sis <- lapply(cdfs, getSnpInformation)
print(sis)
acs <- lapply(lapply(cdfs, getChipType), FUN=function(chipType) {
AromaCellSequenceFile$byChipType(chipType)})
print(acs)
cesNList <- list()
chipType <- chipTypes[1]
cs <- AffymetrixCelSet$byName(dataSetName,chipType=chipType)
cs <- extract(cs,!isDuplicated(cs))
print(cs)
acc <- AllelicCrosstalkCalibration(cs,model="CRMAv2");
print(acc);
csAcc <- process(acc, verbose=log);
bpn <- BasePositionNormalization(csAcc,target="zero")
print(bpn)
csN <- process(bpn,verbose=log)
plm <- RmaCnPlm(csN,mergeStrands=TRUE, combineAlleles=TRUE, shift=
+300);
print(plm);
fit(plm, verbose=log);
if (length(findUnitsTodo(plm)) > 0) {
units <- fitCnProbes(plm, verbose=verbose)
str(units)
units <- fit(plm, verbose=verbose)
str(units)
}
ces <- getChipEffectSet(plm)
print(ces)
fln <- FragmentLengthNormalization(ces, target="zero")
print(fln)
cesNList[[chipType]] <- process(fln, verbose=verbose)
######################################################################
####
#-#
# This is for the second chipType
chipType <- chipTypes[2]
cs <- AffymetrixCelSet$byName(dataSetName,chipType=chipType)
cs <- extract(cs,!isDuplicated(cs))
print(cs)
acc <- AllelicCrosstalkCalibration(cs,model="CRMAv2");
print(acc);
csAcc <- process(acc, verbose=log);
bpn <- BasePositionNormalization(csAcc,target="zero")
print(bpn)
csN <- process(bpn,verbose=log);
plm <- RmaCnPlm(csN,mergeStrands=TRUE, combineAlleles=TRUE, shift=
+300);
print(plm);
fit(plm, verbose=log);
if (length(findUnitsTodo(plm)) > 0) {
units <- fitCnProbes(plm, verbose=verbose)
str(units)
units <- fit(plm, verbose=verbose)
str(units)
}
ces <- getChipEffectSet(plm)
print(ces);
ces <- getChipEffectSet(plm)
print(ces)
fln <- FragmentLengthNormalization(ces, target="zero")
print(fln)
cesNList[[chipType]] <- process(fln, verbose=verbose)
============================================================
cesNList is my CnChipEffectSet
Now my CnChipEffectSet: looks like this
$Mapping250K_Nsp
CnChipEffectSet:
Name: Test
Tags: ACC,-XY,BPN,-XY,RMA,+300,A+B,FLN,-XY
Path: plmData/Test,ACC,-XY,BPN,-XY,RMA,+300,A+B,FLN,-XY/
Mapping250K_Nsp
Platform: Affymetrix
Chip type: Mapping250K_Nsp,monocell
Number of arrays: 80
Names: AA-HGG024, AA-HGG045, ..., OT-HGG155
Time period: 2010-07-14 15:46:23 -- 2010-07-14 15:46:40
Total file size: 764.52MB
RAM: 0.14MB
Parameters: (probeModel: chr "pm", mergeStrands: logi TRUE,
combineAlleles: logi TRUE)
$Mapping250K_Sty
CnChipEffectSet:
Name: Test
Tags: ACC,-XY,BPN,-XY,RMA,+300,A+B,FLN,-XY
Path: plmData/Test,ACC,-XY,BPN,-XY,RMA,+300,A+B,FLN,-XY/
Mapping250K_Sty
Platform: Affymetrix
Chip type: Mapping250K_Sty,monocell
Number of arrays: 79
Names: AA-HGG024, AA-HGG045, ..., OT-HGG155
Time period: 2010-07-15 17:19:56 -- 2010-07-15 17:20:13
Total file size: 687.18MB
RAM: 0.14MB
Parameters: (probeModel: chr "pm", mergeStrands: logi TRUE,
combineAlleles: logi TRUE)
=================================================================
To extract the subset of arrays from cesNList
RefCes <- extract(cesNList, 49:77)
Error in list(`extract(cesNList, 49:77)` = <environment>,
`extract.default(cesNList, 49:77)` = <environment>, :
[2010-07-15 22:05:21] Exception: Do not know how to unwrap object:
list
at throw(Exception(...))
at throw.default("Do not know how to unwrap object: ", class(x)[1])
at throw("Do not know how to unwrap object: ", class(x)[1])
at extract.default(cesNList, 49:77)
at extract(cesNList, 49:77)
==============================================================
I also tried to first extract the array names I want to use as
reference set and I did this:
for (chiptype in names(cesNList)) {
ces <- cesNList[[chiptype]];
cesnames <- getNames(ces); }
refcols<- cesnames[49:77]
extract(cesNList,refcols)
extract(cesNList,refcols)
Error in list(`extract(cesNList, refcols)` = <environment>,
`extract.default(cesNList, refcols)` = <environment>, :
[2010-07-15 22:34:24] Exception: Do not know how to unwrap object:
list
at throw(Exception(...))
at throw.default("Do not know how to unwrap object: ", class(x)[1])
at throw("Do not know how to unwrap object: ", class(x)[1])
at extract.default(cesNList, refcols)
at extract(cesNList, refcols)
Since the CnChipEffectSet is a list of two enzyme set, how do I
extract out the subset of samples for both enzymes and do the
downstream analysis such as:
ceR <- getAverageFile(RefCes, verbose=verbose)
cesT <- extract(cesNList,1:48)
cbs <- CbsModel(ceR, cesT)
==============================================================
attached base packages:
[1] stats graphics grDevices datasets utils methods
base
other attached packages:
[1] DNAcopy_1.18.0 preprocessCore_1.6.0
aroma.affymetrix_1.5.0
[4] aroma.apd_0.1.7 affxparser_1.16.0
R.huge_0.2.0
[7] aroma.core_1.5.0 aroma.light_1.16.0
matrixStats_0.2.1
[10] R.rsp_0.3.6 R.cache_0.3.0
R.filesets_0.8.1
[13] digest_0.4.2 R.utils_1.4.0
R.oo_1.7.2
[16] R.methodsS3_1.2.0
Thanks
Manisha
