Hmm... first run this in a fresh R session:
library("aroma.affymetrix");
cdf <- AffymetrixCdfFile$byChipType("GenomeWideSNP_6", tags="Full");
csR <- AffymetrixCelSet$byName("test", cdf=cdf);
acc <- AllelicCrosstalkCalibration(csR, model="CRMAv2");
csC <- process(acc, verbose=verbose);
bpn <- BasePositionNormalization(csC, target="zero");
csN <- process(bpn, verbose=verbose);
then what's the output of:
print(csN);
print(getFullNames(csN));
cdf2 <- getCdf(csN);
stopifnot(identical(getChecksum(cdf2), getChecksum(cdf))); # IMPORTANT
If you get an error above, what is the output of print(cdf2) and
getChecksum(cdf2)? If not, continue:
plm <- AvgCnPlm(csN, mergeStrands=TRUE, combineAlleles=TRUE);
units <- findUnitsTodo(plm);
str(units);
## int [1:934968] 622 623 624 625 626 627 628 629 630 631 ...
Do you get the same? If so, continue:
units2 <- fit(plm, verbose=-10);
You should get something like the following, except from the
dataset/sample names (if not, let me know):
## Fitting model of class AvgCnPlm...
## AvgCnPlm:
## Data set: GSE13372
## Chip type: GenomeWideSNP_6,Full
## Input tags: testset,ACC,ra,-XY,BPN,-XY
## Output tags: testset,ACC,ra,-XY,BPN,-XY,AVG,A+B
## Parameters: {probeModel: chr "pm", shift: num 0, flavor: chr
"median", mergeStrands: logi TRUE, combineAlleles: logi TRUE}
## Path: plmData/GSE13372,testset,ACC,ra,-XY,BPN,-XY,AVG,A+B/GenomeWideSNP_6
## RAM: 0.01MB
## Identifying non-estimated units...
## Identifying non-fitted units in chip-effect file...
## Pathname:
plmData/GSE13372,testset,ACC,ra,-XY,BPN,-XY,AVG,A+B/GenomeWideSNP_6/GSM337708,chipEffects.CEL
## Found indices cached on file
## Reading data for these 1881415 cells...
## Reading data for these 1881415 cells...done
## Looking for stdvs <= 0 indicating non-estimated units:
## int [1:934968] 622 623 624 625 626 627 628 629 630 631 ...
## Identifying non-fitted units in chip-effect file...done
## Identifying non-estimated units...done
## Getting model fit for 934968 units.
## Identifying unit types:...
## Units:
## int [1:934968] 622 623 624 625 626 627 628 629 630 631 ...
## Unit types:
## atomic [1:934968] 2 2 2 2 2 2 2 2 2 2 ...
## - attr(*, "types")= Named int [1:8] 0 1 2 3 4 5 6 7
## ..- attr(*, "names")= chr [1:8] "unknown" "expression"
"genotyping" "resequencing" ...
## unitTypes
## 2
## 934968
## Unique unit types:
## genotyping
## 2
## Identifying unit types:...done
## Setting up parameter sets...
## Creating CEL file...
## Chip type: GenomeWideSNP_6,Full
## Pathname:
plmData/GSE13372,testset,ACC,ra,-XY,BPN,-XY,AVG,A+B/GenomeWideSNP_6/probeAffinities.CEL
## Returning already existing file.
## Creating CEL file...done
## used (Mb) gc trigger (Mb) max used (Mb)
## Ncells 549305 29.4 1606180 85.8 13015638 695.2
## Vcells 7692698 58.7 23004541 175.6 40154683 306.4
## Setting up parameter sets...done
## Fitting AvgCnPlm for each unit type separately...
## Unit types:
## genotyping
## 2
## Unit type #1 ('genotyping') of 1...
## Unit type: genotyping (code=2)
## Number of units of this type: 934968
## int [1:934968] 622 623 624 625 626 627 628 629 630 631 ...
## Fitting the model by unit dimensions (at least for the large classes)...
## Grouping units into equivalent (unit,group,cell) dimensions...
[...]
What is particular interesting are the outputs of your unit types and
unit indices.
/Henrik
On Mon, Nov 26, 2012 at 10:45 AM, Ioana Cutcutache
<ioana.cutcuta...@gmail.com> wrote:
>> library("aroma.affymetrix")
>> log <- verbose <- Arguments$getVerbose(-8, timestamp=TRUE)
>> options(digits=4)
>> cdf <- AffymetrixCdfFile$byChipType("GenomeWideSNP_6", tags="Full")
>> print(cdf)
>> gi <- getGenomeInformation(cdf)
>> print(gi)
>> si <- getSnpInformation(cdf)
>> print(si)
>> acs <- AromaCellSequenceFile$byChipType(getChipType(cdf, fullname=FALSE))
>> print(acs)
>> cdf <- AffymetrixCdfFile$byChipType("GenomeWideSNP_6", tags="Full")
>> csR <- AffymetrixCelSet$byName("test", cdf=cdf)
>> print(csR)
>> acc <- AllelicCrosstalkCalibration(csR, model="CRMAv2")
>> print(acc)
>> csC <- process(acc, verbose=verbose)
>> print(csC)
>> bpn <- BasePositionNormalization(csC, target="zero")
>> print(bpn)
>> csN <- process(bpn, verbose=verbose)
>> print(csN)
--
When reporting problems on aroma.affymetrix, make sure 1) to run the latest
version of the package, 2) to report the output of sessionInfo() and
traceback(), and 3) to post a complete code example.
You received this message because you are subscribed to the Google Groups
"aroma.affymetrix" group with website http://www.aroma-project.org/.
To post to this group, send email to aroma-affymetrix@googlegroups.com
To unsubscribe and other options, go to http://www.aroma-project.org/forum/
