Hi, I cannot reproduce this. First, it is not clear from your message whether it is only this data set that cause problems or all data sets you're trying including the ones you're saying used to work.
Second, start by verifying that your all your files are the same as
mine. Compare your output with mine below:
library("aroma.affymetrix")
verbose <- Arguments$getVerbose(-8, timestamp=TRUE)
# The Affymetrix Chip Definition File
cdf <- AffymetrixCdfFile$byChipType("Mapping250K_Nsp")
print(cdf)
## AffymetrixCdfFile:
## Path: annotationData/chipTypes/Mapping250K_Nsp
## Filename: Mapping250K_Nsp.cdf
## File size: 185.45 MB (194455495 bytes)
## Chip type: Mapping250K_Nsp
## RAM: 0.00MB
## File format: v4 (binary; XDA)
## Dimension: 2560x2560
## Number of cells: 6553600
## Number of units: 262338
## Cells per unit: 24.98
## Number of QC units: 6
print(getChecksum(cdf))
## [1] "59ae263311a2cf63b8d1b9b4cc7d663b"
# Probe sequences
acs <- getAromaCellSequenceFile(cdf)
print(acs)
## AromaCellSequenceFile:
## Name: Mapping250K_Nsp
## Tags: HB20080710
## Full name: Mapping250K_Nsp,HB20080710
## Pathname:
annotationData/chipTypes/Mapping250K_Nsp/Mapping250K_Nsp,HB20080710.acs
## File size: 162.50 MB (170394014 bytes)
## ...
print(getChecksum(acs))
## [1] "b2eee634d101e645cdf616aaf1eb15f7"
# Genome positions for the units in the CDF
ugp <- getAromaUgpFile(cdf)
print(ugp)
## AromaUgpFile:
## Name: Mapping250K_Nsp
## Tags: na31,HB20101007
## Full name: Mapping250K_Nsp,na31,HB20101007
## Pathname:
annotationData/chipTypes/Mapping250K_Nsp/Mapping250K_Nsp,na31,HB20101007.ugp
## File size: 1.25 MB (1312308 bytes)
## ...
print(getChecksum(ugp))
## [1] "aecffa9648f9f4fdebecf2050d9c304a"
# Setup the data set
csR <- AffymetrixCelSet$byName("GSE51265", cdf=cdf)
# Work on the reported CEL file
csR <- extract(csR, "GSM1241436")
print(csR)
## AffymetrixCelSet:
## Name: GSE51265
## Tags:
## Path: rawData/GSE51265/Mapping250K_Nsp
## Platform: Affymetrix
## Chip type: Mapping250K_Nsp
## Number of arrays: 1
## Names: GSM1241436_110830-250K_scc1 [1]
## Time period: 2011-09-07 14:34:52 -- 2011-09-07 14:34:52
## Total file size: 62.64MB
## RAM: 0.01MB
cf <- getFile(csR, 1)
print(cf)
## AffymetrixCelFile:
## Name: GSM1241436_110830-250K_scc1
## Tags:
## Full name: GSM1241436_110830-250K_scc1
## Pathname: rawData/GSE51265/Mapping250K_Nsp/GSM1241436_110830-250K_scc1.CEL
## File size: 62.64 MB (65686370 bytes)
print(getChecksum(cf))
## [1] "beff390913b79fa4b7cd298125aa66a4"
# CRMAv2 crosstalk calibration
acc <- AllelicCrosstalkCalibration(csR, model="CRMAv2")
print(acc)
## AllelicCrosstalkCalibration:
## Data set: GSE51265
## Input tags:
## User tags: *
## Asterisk ('*') tags: ACC,-XY
## Output tags: ACC,-XY
## Number of files: 1 (62.64MB)
## Platform: Affymetrix
## Chip type: Mapping250K_Nsp
## Algorithm parameters: {rescaleBy: chr "groups", targetAvg: num
[1:2] 2200 2200,
## subsetToAvg: int [1:6409592] 1 2 3 4 5 6 7 8 9 10 ..., mergeShifts:
logi TRUE,
## B: int 1, flavor: chr "sfit", algorithmParameters:List of 3, ..$
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/GSE51265,ACC,-XY/Mapping250K_Nsp
## Is done: FALSE
## RAM: 24.46MB
(BTW, '*,probeSeqs.txt' files can be deleted; they have been replaced
by *.acs files since a long time ago.)
Next, lets look at the verbose output to make sure the
AromaCellSequenceFile is used to infer probe sequences;
csC <- process(acc, verbose=verbose)
20140104 13:43:08|Calibrating data set for allelic cross talk...
20140104 13:43:08| Compressing model parameter to a short format...
20140104 13:43:08| Compressing model parameter to a short format...done
20140104 13:43:08| Calibrating 1 arrays...
20140104 13:43:08| Path: probeData/GSE51265,ACC,-XY/Mapping250K_Nsp
20140104 13:43:08| Array #1 ('GSM1241436_110830-250K_scc1') of 1...
20140104 13:43:08| Identifying sets of pairs of cell indices...
20140104 13:43:08| Chip type: Mapping250K_Nsp
20140104 13:43:08| Merge shifts: TRUE
20140104 13:43:08| Number of nucleotides: 1
20140104 13:43:08| Locating AromaCellSequenceFile...
20140104 13:43:08| Chip type: Mapping250K_Nsp
20140104 13:43:08| Number of cells: 6553600
AromaCellSequenceFile:
Name: Mapping250K_Nsp
Tags: HB20080710
Full name: Mapping250K_Nsp,HB20080710
Pathname:
annotationData/chipTypes/Mapping250K_Nsp/Mapping250K_Nsp,HB20080710.acs
File size: 162.50 MB (170394014 bytes)
RAM: 0.00 MB
Number of data rows: 6553600
File format: v1
Dimensions: 6553600x26
Column classes: raw, raw, raw, raw, raw, raw, raw, raw, raw, raw,
raw, raw, raw, raw, raw, raw, raw, raw, raw, raw, raw, raw, raw, raw,
raw, raw
Number of bytes per column: 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1,
1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1
Footer: <createdOn>20080710 20:51:42
PDT</createdOn><platform>Affymetrix</platform><chipType>Mapping250K_Nsp</chipType><srcFile><filename>Mapping250K_Nsp_probe_tab</filename><filesize>192825014</filesize><checksum>bf2921824b9c14285f12b4bea18babda</checksum></srcFile>
Chip type: Mapping250K_Nsp
Platform: Affymetrix
20140104 13:43:08| Locating AromaCellSequenceFile...done
20140104 13:43:08| Identifying cell indices for all non-SNP units...
20140104 13:43:08| Non-SNP units:...
int(0)
20140104 13:43:08| Non-SNP cells:...
NULL
20140104 13:43:08| Non-SNP cells:...done
20140104 13:43:08| Identifying the probe pairs...
20140104 13:43:08| Units:
NULL
20140104 13:43:08| Checking for cached results...
20140104 13:43:09| Found cached results
20140104 13:43:09| Checking for cached results...done
20140104 13:43:09| Identifying the probe pairs...done
20140104 13:43:09| Probe shifts:
[1] 0
20140104 13:43:09| Identifying groups of SNP nucleotide sequence pairs...
20140104 13:43:09| Checking for cached results...
20140104 13:43:09| Found cached results
20140104 13:43:09| Checking for cached results...done
20140104 13:43:09| Identifying groups of SNP nucleotide sequence
pairs...done
20140104 13:43:09| Non-SNP units:...done
20140104 13:43:09| Identifying cell indices for all non-SNP units...done
20140104 13:43:09| Identifying sets of pairs of cell indices...done
20140104 13:43:09| setsOfProbes:
List of 2
$ snps :List of 7
..$ A/C : int [1:129194, 1:2] 5555562 640260 6430798 890622
858750 4681948 347160 5718766 2746760 2790782 ...
.. ..- attr(*, "dimnames")=List of 2
.. .. ..$ : NULL
.. .. ..$ : chr [1:2] "A" "C"
..$ A/G : int [1:519999, 1:2] 4969704 4677672 4787718 5185370
1363100 4109892 1558340 1352256 1332280 4969616 ...
.. ..- attr(*, "dimnames")=List of 2
.. .. ..$ : NULL
.. .. ..$ : chr [1:2] "A" "G"
..$ A/T : int [1:107590, 1:2] 1028670 3832004 5665036 1832744
4167500 4571986 4938090 747094 2207654 5855716 ...
.. ..- attr(*, "dimnames")=List of 2
.. .. ..$ : NULL
.. .. ..$ : chr [1:2] "A" "T"
..$ C/G : int [1:156840, 1:2] 4747206 3909704 1725666 600232
416088 1138554 6393394 6389120 555046 2960654 ...
.. ..- attr(*, "dimnames")=List of 2
.. .. ..$ : NULL
.. .. ..$ : chr [1:2] "C" "G"
..$ C/T : int [1:572339, 1:2] 3789122 5491344 768382 4974648
387402 2086744 1183506 5290380 6464728 6121838 ...
.. ..- attr(*, "dimnames")=List of 2
.. .. ..$ : NULL
.. .. ..$ : chr [1:2] "C" "T"
..$ G/T : int [1:124838, 1:2] 2968724 1545656 2540860 5758784
3927738 3915584 4695222 2062772 6258084 4709566 ...
.. ..- attr(*, "dimnames")=List of 2
.. .. ..$ : NULL
.. .. ..$ : chr [1:2] "G" "T"
..$ missing: int [1:700, 1:2] 3365154 3362594 3360034 3357474
3354914 3352354 3349794 3329314 3326754 3324194 ...
$ nonSNPs: NULL
- attr(*, "version")= num 4
[...]
That 'setsOfProbes' should list the same cell/probe indices for you.
Still, If everything is the same this far, then compare your to my
attached ACC verbose output and check where things differ goes wrong.
/Henrik
On Sat, Jan 4, 2014 at 8:21 AM, Hans-Ulrich
<hans-ulrich.kl...@uni-muenster.de> wrote:
> Dear aroma group,
>
> I tried to apply CRMAv2 on my 250K_Nsp array data set. The same script ran
> without problems on another 250K data set a couple of months ago and I can
> not figure out what is going wrong with my current data set. I downloaded
> two public CEL files and got the same error. Here are the details:
>
> I used these two CEL files as test data set:
> wget
> ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1241nnn/GSM1241436/suppl/GSM1241436_110830-250K_scc1.CEL.gz
> wget
> ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1241nnn/GSM1241437/suppl/GSM1241437_110830-250K_scc2.CEL.gz
>
> My annotationData/chipTypes/Mapping250K_Nsp folder contains these files
> Mapping250K_Nsp.cdf
> Mapping250K_Nsp,HB20080710.acs
> Mapping250K_Nsp,na31,HB20101007.ugp
> Mapping250K_Nsp,HB20080621,probeSeqs.txt
> Mapping250K_Nsp,na31,HB20101007.ufl
> which I obtained from
> http://www.aroma-project.org/data/annotationData/chipTypes/Mapping250K_Nsp/.
>
> This is my script and the respective error message:
>
> library("aroma.affymetrix")
> verbose <- Arguments$getVerbose(-8, timestamp=TRUE)
> Sys.setlocale(locale="C")
>
> chipType <- "Mapping250K_Nsp"
>
> cdf <- AffymetrixCdfFile$byChipType(chipType)
> gi <- getGenomeInformation(cdf)
> si <- getSnpInformation(cdf)
> acs <- AromaCellSequenceFile$byChipType(getChipType(cdf, fullname=FALSE))
>
> csR <- AffymetrixCelSet$byName("testdata", cdf=cdf)
> print(csR)
>
> acc <- AllelicCrosstalkCalibration(csR, model="CRMAv2")
> print(acc)
> csC <- process(acc, verbose=verbose)
>
> [...]
>
> [2014-01-04 16:51:16] Exception: Cannot rescale to target average. After
> taking the intersect of the subset of cells to be used, there are no cells
> left.
>
> at #06. rescaleByGroups.AllelicCrosstalkCalibration(this, yAll = yAll,
> params = params, ...)
> - rescaleByGroups.AllelicCrosstalkCalibration() is in environment
> 'aroma.affymetrix'
>
> at #05. rescaleByGroups(this, yAll = yAll, params = params, ...)
> - rescaleByGroups() is in environment 'aroma.affymetrix'
>
> at #04. rescale.AllelicCrosstalkCalibration(this, yAll = yAll, params =
> params,
> setsOfProbes = setsOfProbes, verbose = less(verbose))
> - rescale.AllelicCrosstalkCalibration() is in environment
> 'aroma.affymetrix'
>
> at #03. rescale(this, yAll = yAll, params = params, setsOfProbes =
> setsOfProbes,
> verbose = less(verbose))
> - rescale() is in environment 'aroma.core'
>
> at #02. process.AllelicCrosstalkCalibration(acc, verbose = verbose)
> - process.AllelicCrosstalkCalibration() is in environment
> 'aroma.affymetrix'
>
> at #01. process(acc, verbose = verbose)
> - process() is in environment 'aroma.core'
>
> Error: Cannot rescale to target average. After taking the intersect of the
> subset of cells to be used, there are no cells left.
> In addition: Warning message:
> In fcn(...) : Packages reordered in search path: package:affxparser
> 20140104 16:51:16| Array #1 ('GSM1241436_110830-250K_scc1') of 2...done
> 20140104 16:51:16| Calibrating 2 arrays...done
> 20140104 16:51:16|Calibrating data set for allelic cross talk...done
>
> traceback()
> 11: stop(cond)
> 10: throw.Exception(Exception(...))
> 9: throw(Exception(...))
> 8: throw.default("Cannot rescale to target average. After taking the
> intersect of the subset of cells to be used, there are no cells left.")
> 7: throw("Cannot rescale to target average. After taking the intersect of
> the subset of cells to be used, there are no cells left.")
> 6: rescaleByGroups.AllelicCrosstalkCalibration(this, yAll = yAll,
> params = params, ...)
> 5: rescaleByGroups(this, yAll = yAll, params = params, ...)
> 4: rescale.AllelicCrosstalkCalibration(this, yAll = yAll, params = params,
> setsOfProbes = setsOfProbes, verbose = less(verbose))
> 3: rescale(this, yAll = yAll, params = params, setsOfProbes = setsOfProbes,
> verbose = less(verbose))
> 2: process.AllelicCrosstalkCalibration(acc, verbose = verbose)
> 1: process(acc, verbose = verbose)
>
> sessionInfo()
> R version 3.0.1 (2013-05-16)
> Platform: x86_64-pc-linux-gnu (64-bit)
>
> locale:
> [1] LC_CTYPE=C LC_NUMERIC=C
> [3] LC_TIME=C LC_COLLATE=C
> [5] LC_MONETARY=C LC_MESSAGES=en_US.UTF-8
> [7] LC_PAPER=C 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] sfit_0.3.0 aroma.light_1.32.0 matrixStats_0.8.12
> [4] aroma.affymetrix_2.11.1 aroma.core_2.11.0 R.devices_2.7.2
> [7] R.filesets_2.3.0 R.utils_1.28.4 R.oo_1.15.8
> [10] affxparser_1.34.0 R.methodsS3_1.5.2
>
> loaded via a namespace (and not attached):
> [1] DNAcopy_1.36.0 PSCBS_0.40.2 R.cache_0.9.0 R.huge_0.6.0
> [5] R.rsp_0.9.28 aroma.apd_0.4.0 digest_0.6.4 tools_3.0.1
>
>
> Interestingly, the allelic crosstalk calibration works when I set the
> parameter subsetToAvg=NULL. However, I does not make sense to me why it does
> not work when probes on chromosomes X and Y were omitted (which is the
> default).
>
> Any help is welcome.
>
> Best regards,
> Hans
>
> --
> --
> 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/
>
> ---
> You received this message because you are subscribed to the Google Groups
> "aroma.affymetrix" group.
> To unsubscribe from this group and stop receiving emails from it, send an
> email to aroma-affymetrix+unsubscr...@googlegroups.com.
> For more options, visit https://groups.google.com/groups/opt_out.
--
--
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/
---
You received this message because you are subscribed to the Google Groups
"aroma.affymetrix" group.
To unsubscribe from this group and stop receiving emails from it, send an email
to aroma-affymetrix+unsubscr...@googlegroups.com.
For more options, visit https://groups.google.com/groups/opt_out.
ACC.log
Description: Binary data
