Hello,
I'd like to perform background correction on a HuEx-1_0-st-v2 CEL file that
I've previously converted from xda binary format (Affymetrix v4) to ASCII
text format (Affymetrix v3). I did the file format conversion because aroma
does not work xda-format CEL files, and I used apt-cel-convert provided by
Affymetrix Power Tools for this conversion. There are several error
messages that come up when I use RmaBackgroundCorrection() on the file,
some of which are:
20141229 20:59:04| Cannot create CEL file of version 4
(probeData/myData,RBC/HuEx-1_0-st-v2/EA_BT549.CEL.tmp). Template CEL file
is of version 3: rawData/myData/HuEx-1_0-st-v2/EA_BT549.CEL
20141229 21:00:50| Method 'create'...done
AffymetrixCelFile:
Name: EA_BT549.CEL.tmp
Tags:
Full name: EA_BT549.CEL.tmp
Pathname: probeData/myData,RBC/HuEx-1_0-st-v2/EA_BT549.CEL.tmp
File size: 62.50 MB (65536700 bytes)
RAM: 0.00 MB
File format: v4 (binary; XDA)
Platform: Affymetrix
Chip type: HuEx-1_0-st-v2,fullR3,A20071112,EP
Timestamp: 2014-12-29 20:59:04
20141229 21:00:51| Creating CEL file...done
20141229 21:00:51| Creating CEL file for results, if missing...done
20141229 21:00:51| Writing adjusted intensities...
Error in if (r[1] < 1 || r[2] > nbrOfCells) { :
missing value where TRUE/FALSE needed
20141229 21:00:51| Writing adjusted intensities...done
20141229 21:00:51| Writing adjusted probe signals...done
20141229 21:00:51| Array #1 ('EA_BT549') of 1...done
20141229 21:00:51|Background correcting data set...done
I've provided the full report of the process in the attachment. From the
error message, it seems that the information from the original v4 file has
been retained somehow. Is there an option I can use in the
RmaBackgroundCorrection() function to fix this? Steps I used prior to this
were those found in the aroma page (additionally, I've used this on my v3
data many times before with no problems):
chipType <- "HuEx-1_0-st-v2"
cdf <- AffymetrixCdfFile$byChipType(chipType, tags = "fullR3,A20071112,EP")
verbose <- Arguments$getVerbose(-8, timestamp=TRUE)
cs <- AffymetrixCelSet$byName("myData", cdf=cdf)
bc <- RmaBackgroundCorrection(cs)
csBC <- process(bc, verbose = verbose)
-----------------------------------------------------
> sessionInfo()
R version 3.0.2 (2013-09-25)
Platform: x86_64-redhat-linux-gnu (64-bit)
locale:
[1] C
attached base packages:
[1] splines grid parallel stats graphics grDevices utils
datasets methods base
other attached packages:
[1] Hmisc_3.14-6 Formula_1.1-2 survival_2.37-7
lattice_0.20-29 aroma.light_2.0.0
[6] matrixStats_0.10.0 aroma.affymetrix_2.12.8 aroma.core_2.12.8
R.devices_2.12.0 R.filesets_2.6.0
[11] affy_1.40.0 Biobase_2.22.0 BiocGenerics_0.8.0
affxparser_1.34.2 R.utils_1.34.0
[16] R.oo_1.18.2 R.methodsS3_1.6.2
loaded via a namespace (and not attached):
[1] BiocInstaller_1.12.1 DNAcopy_1.36.0 PSCBS_0.43.0
R.cache_0.11.0 R.huge_0.8.0 R.rsp_0.19.6
[7] RColorBrewer_1.1-2 acepack_1.3-3.3 affyio_1.30.0
aroma.apd_0.5.0 base64enc_0.1-2 cluster_1.15.3
[13] digest_0.6.7 foreign_0.8-61 latticeExtra_0.6-26
nnet_7.3-8 preprocessCore_1.24.0 rpart_4.1-8
[19] tools_3.0.2 zlibbioc_1.8.0
Many thanks in advance.
Aish
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20141229 20:58:37|Background correcting data set...
20141229 20:58:37| Number of arrays: 1
20141229 20:58:37| Array #1 ('EA_BT549') of 1...
20141229 20:58:43| Adjusting PM signals only
20141229 20:58:43| Obtaining signals...
20141229 20:58:56| Obtaining signals...done
20141229 20:58:56| Applying normal+exponential signal model...
20141229 20:58:58| Applying normal+exponential signal model...done
20141229 20:58:58| Writing adjusted probe signals...
20141229 20:58:58| Adding temporary suffix from file...
20141229 20:58:58| Pathname: probeData/myData,RBC/HuEx-1_0-st-v2/EA_BT549.CEL
20141229 20:58:58| Suffix: .tmp
20141229 20:58:58| Rename existing file?: FALSE
20141229 20:58:58| Temporary pathname:
probeData/myData,RBC/HuEx-1_0-st-v2/EA_BT549.CEL.tmp
20141229 20:58:58| Adding temporary suffix from file...done
20141229 20:58:58| Creating CEL file for results, if missing...
20141229 20:58:58| Creating CEL file...
20141229 20:58:58| Chip type: HuEx-1_0-st-v2,fullR3,A20071112,EP
20141229 20:58:58| Pathname:
probeData/myData,RBC/HuEx-1_0-st-v2/EA_BT549.CEL.tmp
20141229 20:58:58| Adding temporary suffix from file...
20141229 20:58:58| Pathname:
probeData/myData,RBC/HuEx-1_0-st-v2/EA_BT549.CEL.tmp
20141229 20:58:58| Suffix: .tmp
20141229 20:58:58| Rename existing file?: FALSE
20141229 20:58:58| Temporary pathname:
probeData/myData,RBC/HuEx-1_0-st-v2/EA_BT549.CEL.tmp.tmp
20141229 20:58:58| Adding temporary suffix from file...done
20141229 20:58:58| Method 'copy'...
20141229 20:59:04| Cannot create CEL file of version 4
(probeData/myData,RBC/HuEx-1_0-st-v2/EA_BT549.CEL.tmp). Template CEL file is of
version 3: rawData/myData/HuEx-1_0-st-v2/EA_BT549.CEL
20141229 20:59:04| Method 'copy'...done
20141229 20:59:04| Method 'create'...
20141229 20:59:04| Creating an empty temporary CEL file...
20141229 20:59:04| Creating an empty temporary CEL file...done
20141229 20:59:04| Copying CEL data...
20141229 20:59:04| lapplyInChunks()...
20141229 20:59:05| Number of elements per chunk: 1e+06
20141229 20:59:05| Chunk #1 of 7...
20141229 20:59:05| Elements:
int [1:1000000] 1 2 3 4 5 6 7 8 9 10 ...
20141229 20:59:05| Reading subset of data from source CEL file...
20141229 20:59:18| Reading subset of data from source CEL file...done
20141229 20:59:18| Writing data to new CEL file...
20141229 20:59:22| Writing data to new CEL file...done
used (Mb) gc trigger (Mb) max used (Mb)
Ncells 867866 46.4 1368491 73.1 1368491 73.1
Vcells 18702746 142.7 39754025 303.3 39715885 303.1
20141229 20:59:22| Chunk #1 of 7...done
20141229 20:59:22| Chunk #2 of 7...
20141229 20:59:22| Elements:
int [1:1000000] 1000001 1000002 1000003 1000004 1000005 1000006
1000007 1000008 1000009 1000010 ...
20141229 20:59:22| Reading subset of data from source CEL file...
20141229 20:59:35| Reading subset of data from source CEL file...done
20141229 20:59:35| Writing data to new CEL file...
20141229 20:59:37| Writing data to new CEL file...done
used (Mb) gc trigger (Mb) max used (Mb)
Ncells 867878 46.4 1368491 73.1 1368491 73.1
Vcells 18202754 138.9 39754025 303.3 39715885 303.1
20141229 20:59:37| Chunk #2 of 7...done
20141229 20:59:37| Chunk #3 of 7...
20141229 20:59:37| Elements:
int [1:1000000] 2000001 2000002 2000003 2000004 2000005 2000006
2000007 2000008 2000009 2000010 ...
20141229 20:59:37| Reading subset of data from source CEL file...
20141229 20:59:50| Reading subset of data from source CEL file...done
20141229 20:59:50| Writing data to new CEL file...
20141229 20:59:52| Writing data to new CEL file...done
used (Mb) gc trigger (Mb) max used (Mb)
Ncells 867879 46.4 1368491 73.1 1368491 73.1
Vcells 17702755 135.1 39754025 303.3 39715885 303.1
20141229 20:59:52| Chunk #3 of 7...done
20141229 20:59:52| Chunk #4 of 7...
20141229 20:59:52| Elements:
int [1:1000000] 3000001 3000002 3000003 3000004 3000005 3000006
3000007 3000008 3000009 3000010 ...
20141229 20:59:52| Reading subset of data from source CEL file...
20141229 21:00:05| Reading subset of data from source CEL file...done
20141229 21:00:05| Writing data to new CEL file...
20141229 21:00:06| Writing data to new CEL file...done
used (Mb) gc trigger (Mb) max used (Mb)
Ncells 867880 46.4 1368491 73.1 1368491 73.1
Vcells 17202756 131.3 39754025 303.3 39715885 303.1
20141229 21:00:07| Chunk #4 of 7...done
20141229 21:00:07| Chunk #5 of 7...
20141229 21:00:07| Elements:
int [1:1000000] 4000001 4000002 4000003 4000004 4000005 4000006
4000007 4000008 4000009 4000010 ...
20141229 21:00:07| Reading subset of data from source CEL file...
20141229 21:00:20| Reading subset of data from source CEL file...done
20141229 21:00:20| Writing data to new CEL file...
20141229 21:00:21| Writing data to new CEL file...done
used (Mb) gc trigger (Mb) max used (Mb)
Ncells 867881 46.4 1368491 73.1 1368491 73.1
Vcells 16702757 127.5 39754025 303.3 39715885 303.1
20141229 21:00:21| Chunk #5 of 7...done
20141229 21:00:21| Chunk #6 of 7...
20141229 21:00:21| Elements:
int [1:1000000] 5000001 5000002 5000003 5000004 5000005 5000006
5000007 5000008 5000009 5000010 ...
20141229 21:00:21| Reading subset of data from source CEL file...
20141229 21:00:34| Reading subset of data from source CEL file...done
20141229 21:00:34| Writing data to new CEL file...
20141229 21:00:36| Writing data to new CEL file...done
used (Mb) gc trigger (Mb) max used (Mb)
Ncells 867882 46.4 1368491 73.1 1368491 73.1
Vcells 16202758 123.7 39754025 303.3 39715885 303.1
20141229 21:00:36| Chunk #6 of 7...done
20141229 21:00:36| Chunk #7 of 7...
20141229 21:00:36| Elements:
int [1:553600] 6000001 6000002 6000003 6000004 6000005 6000006
6000007 6000008 6000009 6000010 ...
20141229 21:00:36| Reading subset of data from source CEL file...
20141229 21:00:49| Reading subset of data from source CEL file...done
20141229 21:00:49| Writing data to new CEL file...
20141229 21:00:50| Writing data to new CEL file...done
used (Mb) gc trigger (Mb) max used (Mb)
Ncells 867883 46.4 1368491 73.1 1368491 73.1
Vcells 15033159 114.7 39754025 303.3 39715885 303.1
20141229 21:00:50| Chunk #7 of 7...done
20141229 21:00:50| lapplyInChunks()...done
20141229 21:00:50| Copying CEL data...done
20141229 21:00:50| Dropping temporary suffix from file...
20141229 21:00:50| Temporary pathname:
probeData/myData,RBC/HuEx-1_0-st-v2/EA_BT549.CEL.tmp.tmp
20141229 21:00:50| Suffix: .tmp
20141229 21:00:50| Regular expression for suffix: \.tmp$
20141229 21:00:50| Pathname:
probeData/myData,RBC/HuEx-1_0-st-v2/EA_BT549.CEL.tmp
20141229 21:00:50| Renaming existing file...
20141229 21:00:50| Result: TRUE
20141229 21:00:50| Renaming existing file...done
20141229 21:00:50| Dropping temporary suffix from file...done
20141229 21:00:50| Method 'create'...done
AffymetrixCelFile:
Name: EA_BT549.CEL.tmp
Tags:
Full name: EA_BT549.CEL.tmp
Pathname: probeData/myData,RBC/HuEx-1_0-st-v2/EA_BT549.CEL.tmp
File size: 62.50 MB (65536700 bytes)
RAM: 0.00 MB
File format: v4 (binary; XDA)
Platform: Affymetrix
Chip type: HuEx-1_0-st-v2,fullR3,A20071112,EP
Timestamp: 2014-12-29 20:59:04
20141229 21:00:51| Creating CEL file...done
20141229 21:00:51| Creating CEL file for results, if missing...done
20141229 21:00:51| Writing adjusted intensities...
Error in if (r[1] < 1 || r[2] > nbrOfCells) { :
missing value where TRUE/FALSE needed
20141229 21:00:51| Writing adjusted intensities...done
20141229 21:00:51| Writing adjusted probe signals...done
20141229 21:00:51| Array #1 ('EA_BT549') of 1...done
20141229 21:00:51|Background correcting data set...done
--
--
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/
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