Hi Henrik,
So, here is the script with added printouts as you suggested:
options(echo = FALSE,digits=4)
library(aroma.affymetrix)
verbose <- Verbose(threshold=-8, timestamp=TRUE);
name="pediatric_HGG"
chipTypes <- c("Mapping250K_Nsp", "Mapping250K_Sty")
cesNList <- list()
for(chipType in chipTypes) {
dsList <- doCRMAv2(name, chipType=chipType,
combineAlleles=FALSE, verbose=verbose,plm="RmaCnPlm");
cesNList[[chipType]] <- dsList$total;
}
cat("=========== print(cesNList) ===============\n")
print(cesNList);
cat("=========== str(getFullNames(cesNList[[1]])) ===============\n")
str(getFullNames(cesNList[[1]]));
cat("=========== str(getFullNames(cesNList[[2]])) ===============\n")
str(getFullNames(cesNList[[2]]));
glad <- GladModel(cesNList)
fit(glad)
cat("=========== print(glad) ===============\n")
print(glad);
cat("=========== print(getChipTypes(glad)) ===============\n")
print(getChipTypes(glad));
cat("=========== print(nbrOfArrays(glad)) ===============\n")
print(nbrOfArrays(glad));
cat("=========== print(getArrays(glad)); ===============\n")
print(getArrays(glad));
cat("=========== ChromosomeExplorer Setup ===============\n")
ce <- ChromosomeExplorer(glad)
print(ce);
cat("=========== sessionInfo() ===============\n")
sessionInfo()
cat("=========== ChromosomeExplorer Process ===============\n")
process(ce, verbose=verbose)
and here is the output:
.... skipped doCRMAv2() output which seems to be fine.....
20111101 09:20:28|CRMAv2...done
=========== print(cesNList) ===============
$Mapping250K_Nsp
AromaUnitTotalCnBinarySet:
Name: pediatric_HGG
Tags: ACC,-XY,BPN,-XY,RMA,FLN,-XY
Full name: pediatric_HGG,ACC,-XY,BPN,-XY,RMA,FLN,-XY
Number of files: 121
Names: AA-HGG024-250knsp, AA-HGG045-250knsp, AA-HGG052-250knsp, ...,
OT-HGG155-250knsp [121]
Path (to the first file):
totalAndFracBData/pediatric_HGG,ACC,-XY,BPN,-XY,RMA,FLN,-XY/Mapping250K_Nsp
Total file size: 121.14 MB
RAM: 0.13MB
$Mapping250K_Sty
AromaUnitTotalCnBinarySet:
Name: pediatric_HGG
Tags: ACC,-XY,BPN,-XY,RMA,FLN,-XY
Full name: pediatric_HGG,ACC,-XY,BPN,-XY,RMA,FLN,-XY
Number of files: 121
Names: AA-HGG024-250ksty, AA-HGG045-250ksty, AA-HGG052-250ksty, ...,
OT-HGG155-250ksty [121]
Path (to the first file):
totalAndFracBData/pediatric_HGG,ACC,-XY,BPN,-XY,RMA,FLN,-XY/Mapping250K_Sty
Total file size: 110.08 MB
RAM: 0.13MB
=========== str(getFullNames(cesNList[[1]])) ===============
chr [1:121] "AA-HGG024-250knsp,total" "AA-HGG045-250knsp,total" ...
=========== str(getFullNames(cesNList[[2]])) ===============
chr [1:121] "AA-HGG024-250ksty,total" "AA-HGG045-250ksty,total" ...
=========== print(glad) ===============
GladModel:
Name: pediatric_HGG
Tags: ACC,-XY,BPN,-XY,RMA,FLN,-XY
Chip type (virtual): Mapping250K_Nsp+Sty
Path: gladData/pediatric_HGG,ACC,-XY,BPN,-XY,RMA,FLN,-XY/Mapping250K_Nsp+Sty
Number of chip types: 2
Sample & reference file pairs:
Chip type #1 ('Mapping250K_Nsp') of 2:
Sample data set:
AromaUnitTotalCnBinarySet:
Name: pediatric_HGG
Tags: ACC,-XY,BPN,-XY,RMA,FLN,-XY
Full name: pediatric_HGG,ACC,-XY,BPN,-XY,RMA,FLN,-XY
Number of files: 121
Names: AA-HGG024-250knsp, AA-HGG045-250knsp, AA-HGG052-250knsp, ...,
OT-HGG155-250knsp [121]
Path (to the first file):
totalAndFracBData/pediatric_HGG,ACC,-XY,BPN,-XY,RMA,FLN,-XY/Mapping250K_Nsp
Total file size: 121.14 MB
RAM: 0.13MB
Reference data set/file:
<average across arrays>
Chip type #2 ('Mapping250K_Sty') of 2:
Sample data set:
AromaUnitTotalCnBinarySet:
Name: pediatric_HGG
Tags: ACC,-XY,BPN,-XY,RMA,FLN,-XY
Full name: pediatric_HGG,ACC,-XY,BPN,-XY,RMA,FLN,-XY
Number of files: 121
Names: AA-HGG024-250ksty, AA-HGG045-250ksty, AA-HGG052-250ksty, ...,
OT-HGG155-250ksty [121]
Path (to the first file):
totalAndFracBData/pediatric_HGG,ACC,-XY,BPN,-XY,RMA,FLN,-XY/Mapping250K_Sty
Total file size: 110.08 MB
RAM: 0.13MB
Reference data set/file:
<average across arrays>
RAM: 0.00MB
=========== print(getChipTypes(glad)) ===============
Mapping250K_Nsp Mapping250K_Sty
"Mapping250K_Nsp" "Mapping250K_Sty"
=========== print(nbrOfArrays(glad)) ===============
[1] 0
=========== print(getArrays(glad)); ===============
character(0)
=========== ChromosomeExplorer Setup ===============
ChromosomeExplorer:
Name: pediatric_HGG
Tags: ACC,-XY,BPN,-XY,RMA,FLN,-XY
Number of arrays: 0
Path: reports/pediatric_HGG/ACC,-XY,BPN,-XY,RMA,FLN,-XY/Mapping250K_Nsp+Sty/glad
RAM: 0.00MB
=========== sessionInfo() ===============
R version 2.13.2 (2011-09-30)
Platform: x86_64-unknown-linux-gnu (64-bit)
locale:
[1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
[3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8
[5] LC_MONETARY=C LC_MESSAGES=en_US.UTF-8
[7] LC_PAPER=en_US.UTF-8 LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] GLAD_2.14.0 aroma.affymetrix_2.2.0 affxparser_1.24.0
[4] aroma.apd_0.2.0 R.huge_0.3.0 aroma.core_2.2.2
[7] aroma.light_1.21.2 matrixStats_0.3.0 R.rsp_0.6.3
[10] R.cache_0.5.2 R.filesets_1.1.3 digest_0.5.1
[13] R.utils_1.8.5 R.oo_1.8.2 R.methodsS3_1.2.1
=========== ChromosomeExplorer Process ===============
... skipped ...
So, glad object has 0 arrays, this doesn't look right, does it? But why??
Thanks a lot!
Ivan
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