Hi Henrik,
I tested the updated code and got the error message "Exception: Could not
locate a file for this chip type: Mapping250K_Nsp" -- a similar message
showed up at some point previously when I was trying to process SNP 6.0
data, saying "could not locate a file for this chip type: GenomeWideSNP_6".
I checked the annotation files and they are good. And I think my directory
structure is correct too:
working directory: C:\Data\GSE12702_RAW
annotation: C:\Data\GSE12702_RAW\annotationData\chipTypes\Mapping250K_Nsp
raw data: C:\Data\GSE12702_RAW\rawData\GSE12702\Mapping250K_Nsp
Thanks!
-Michelle
>library("aroma.affymetrix");
>cwd="C:/Data/GSE12702_RAW/"
>setwd(cwd)
>dataSet <- "GSE12702";
>chipType <- "Mapping250K_Nsp";
># Load all samples (in case more samples were downloaded)
>csR <- AffymetrixCelSet$byName(dataSet, chipType=chipType);
># Extract tumor-normal pair of interest
>pair <- c(T="GSM318736", N="GSM318737");
>csR <- extract(csR, indexOf(csR, pair));
>print(csR);
AffymetrixCelSet:
Name: GSE12702
Tags:
Path: rawData/GSE12702/Mapping250K_Nsp
Platform: Affymetrix
Chip type: Mapping250K_Nsp
Number of arrays: 2
Names: GSM318736, GSM318737 [2]
Time period: 2008-04-04 14:07:29 -- 2008-04-04 14:39:34
Total file size: 125.31MB
RAM: 0.00MB
> res <- doASCRMAv2(csR, verbose=verbose);
CRMAv2...
Arguments:
combineAlleles: FALSE
arrays:
chr ""
ram:
Data set
AffymetrixCelSet:
Name: GSE12702
Tags:
Path: rawData/GSE12702/Mapping250K_Nsp
Platform: Affymetrix
Chip type: Mapping250K_Nsp
Number of arrays: 2
Names: GSM318736, GSM318737 [2]
Time period: 2008-04-04 14:07:29 -- 2008-04-04 14:39:34
Total file size: 125.31MB
RAM: 0.00MB
CRMAv2/Allelic crosstalk calibration...
AllelicCrosstalkCalibration:
Data set: GSE12702
Input tags:
User tags: *
Asterisk ('*') tags: ACC,-XY
Output tags: ACC,-XY
Number of files: 2 (125.31MB)
Platform: Affymetrix
Chip type: Mapping250K_Nsp
Algorithm parameters: (rescaleBy: chr "groups", targetAvg: num [1:2] 2200
2200, subsetToAvg: chr "-XY", mergeShifts: logi TRUE, B: int 1, flavor: chr
"sfit", algorithmParameters:List of 3, ..$ alpha: num [1:8] 0.1 0.075 0.05
0.03 0.01 0.0025 0.001 0.0001, ..$ q: num 2, ..$ Q: num 98)
Output path: probeData/GSE12702,ACC,-XY/Mapping250K_Nsp
Is done: FALSE
RAM: 0.00MB
Calibrating data set for allelic cross talk...
Compressing model parameter to a short format...
Compressing model parameter to a short format...done
Calibrating 2 arrays...
Path: probeData/GSE12702,ACC,-XY/Mapping250K_Nsp
Array #1 ('GSM318736') of 2...
Error in list(`doASCRMAv2(csR, verbose = verbose)` = <environment>,
`doASCRMAv2.default(csR, verbose = verbose)` = <environment>, :
[2011-11-15 13:02:41] Exception: Could not locate a file for this chip
type: Mapping250K_Nsp
at throw(Exception(...))
at throw.default("Could not locate a file for this chip type: ",
paste(c(chipType, tags), collapse = ","))
at throw("Could not locate a file for this chip type: ",
paste(c(chipType, tags), collapse = ","))
at method(static, ...)
at AromaCellSequenceFile$byChipType(chipType, nbrOfCells = nbrOfCells)
at getSetsOfProbes.AllelicCrosstalkCalibration(this, verbose =
less(verbose, 1))
at getSetsOfProbes(this, verbose = less(verbose, 1))
at process.AllelicCrosstalkCalibration(acc, verbose = verbose)
at process(acc, verbose = verbose)
at doCRMAv2.AffymetrixCelSet(..., combineAlleles = FALSE)
at doCRMAv2(..., combineAlleles = FALSE)
at doASCRMAv2.default(csR, verbose = verbose)
at doASCRMAv2(csR, verbose = verbose)
Array #1 ('GSM318736') of 2...done
Calibrating 2 arrays...done
Calibrating data set for allelic cross talk...done
--
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version of the package, 2) to report the output of sessionInfo() and
traceback(), and 3) to post a complete code example.
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