Re: [aroma.affymetrix] Help needed regarding GCRMA normalization of exon arrays using aroma.affymetrix.....
Hi. On Wed, Sep 29, 2010 at 10:32 AM, Prithish Banerjee prithish.baner...@gmail.com wrote: Respected Dr Bengtsson, Thank you for the help. I have done what you have suggested and the following output is as follows: source(http://aroma-project.org/hbLite.R;); hbInstall(aroma.affymetrix) source(http://aroma-project.org/hbLite.R;); hbInstall(aroma.cn) verbose - Arguments$getVerbose(-10, timestamp=TRUE); dataSet - Exon Data chipType - MoEx-1_0-st-v1 cdf - AffymetrixCdfFile$byChipType(chipType,tags=coreR1,A20080718,MR) print(cdf) ptf - AffymetrixProbeTabFile$byChipType(MoEx-1_0-st-v1); print(ptf) csR - AffymetrixCelSet$byName(dataSet, chipType=chipType) print(csR) cdf - getCdf(csR) cdfS - AffymetrixCdfFile$byChipType(getChipType(cdf, fullname=FALSE)) setCdf(csR, cdfS) bc - GcRmaBackgroundCorrection(csR, type=affinities) print(bc) csB - process(bc, cdf=cdf, ptf=ptf, verbose=verbose) 20100928 22:40:59|Background correcting data set... 20100928 22:41:09| Computing probe affinities... 20100928 22:41:09| Reading saved affinities: probeData/Exon Data,GRBC/MoEx-1_0-st-v1/MoEx-1_0-st-v1-affinities.apa... 20100928 22:41:10| Reading saved affinities: probeData/Exon Data,GRBC/MoEx-1_0-st-v1/MoEx-1_0-st-v1-affinities.apa...done 20100928 22:41:10| RAM: 50.00MB 20100928 22:41:10| Computing probe affinities...done 20100928 22:41:10| Background correcting data set... 20100928 22:41:16| Already background corrected for optical effects 20100928 22:41:16| Background correcting data set...done 20100928 22:41:16| Estimating specific binding parameters... 20100928 22:41:16| Extracting PM indices... 20100928 22:41:16| Reading cell indices from CDF file... 20100928 22:41:16| Pathname: annotationData/chipTypes/MoEx-1_0-st-v1/MoEx-1_0-st-v1.cdf 20100928 22:41:16| Units: NULL 20100928 22:41:16| lapplyInChunks()... 20100928 22:41:16| Number of elements per chunk: 1e+05 20100928 22:41:16| Chunk #1 of 13... 20100928 22:41:16| Elements: int [1:10] 1 2 3 4 5 6 7 8 9 10 ... 20100928 22:41:16| Querying CDF file... 20100928 22:41:20| Querying CDF file...done 20100928 22:41:21| Restructuring... 20100928 22:41:21| Restructuring...done used (Mb) gc trigger (Mb) max used (Mb) Ncells 2058626 110 6907341 368.9 17756025 948.3 Vcells 14800385 113 55506200 423.5 106800686 814.9 20100928 22:41:21| Chunk #1 of 13...done 20100928 22:41:21| Chunk #2 of 13... 20100928 22:41:21| Elements: int [1:10] 11 12 13 14 15 16 17 18 19 100010 ... 20100928 22:41:21| Querying CDF file... 20100928 22:41:25| Querying CDF file...done 20100928 22:41:26| Restructuring... 20100928 22:41:26| Restructuring...done used (Mb) gc trigger (Mb) max used (Mb) Ncells 2058632 110.0 6907341 368.9 17756025 948.3 Vcells 14946933 114.1 44404960 338.8 106800686 814.9 20100928 22:41:26| Chunk #2 of 13...done 20100928 22:41:26| Chunk #3 of 13... 20100928 22:41:26| Elements: int [1:10] 21 22 23 24 25 26 27 28 29 200010 ... 20100928 22:41:26| Querying CDF file... 20100928 22:41:30| Querying CDF file...done 20100928 22:41:30| Restructuring... 20100928 22:41:30| Restructuring...done used (Mb) gc trigger (Mb) max used (Mb) Ncells 2058634 110.0 6907341 368.9 17756025 948.3 Vcells 15101344 115.3 44404960 338.8 106800686 814.9 20100928 22:41:31| Chunk #3 of 13...done 20100928 22:41:31| Chunk #4 of 13... 20100928 22:41:31| Elements: int [1:10] 31 32 33 34 35 36 37 38 39 300010 ... 20100928 22:41:31| Querying CDF file... 20100928 22:41:35| Querying CDF file...done 20100928 22:41:35| Restructuring... 20100928 22:41:35| Restructuring...done used (Mb) gc trigger (Mb) max used (Mb) Ncells 2058634 110.0 6907341 368.9 17756025 948.3 Vcells 15249056 116.4 44404960 338.8 106800686 814.9 20100928 22:41:36| Chunk #4 of 13...done 20100928 22:41:36| Chunk #5 of 13... 20100928 22:41:36| Elements: int [1:10] 41 42 43 44 45 46 47 48 49 400010 ... 20100928 22:41:36| Querying CDF file... 20100928 22:41:40| Querying CDF file...done 20100928 22:41:40| Restructuring... 20100928 22:41:40| Restructuring...done used (Mb) gc trigger (Mb) max used (Mb) Ncells 2058635 110.0 6907341 368.9 17756025 948.3 Vcells 15397125 117.5 44404960 338.8 106800686 814.9 20100928 22:41:40| Chunk #5 of 13...done 20100928 22:41:40| Chunk #6 of 13... 20100928 22:41:40| Elements: int [1:10] 51 52 53 54 55
Re: [aroma.affymetrix] Help needed regarding GCRMA normalization of exon arrays using aroma.affymetrix.....
Respected Dr Bengtsson,
My codes and outputs are as follows:
source(http://aroma-project.org/hbLite.R;);
hbInstall(aroma.affymetrix)
source(http://aroma-project.org/hbLite.R;);
hbInstall(aroma.cn)
verbose - Arguments$getVerbose(-10, timestamp=TRUE);
dataSet - Exon Data
chipType - MoEx-1_0-st-v1
cdf - AffymetrixCdfFile$byChipType(chipType,tags=coreR1,A20080718,MR)
print(cdf)
AffymetrixCdfFile:
Path: annotationData/chipTypes/MoEx-1_0-st-v1
Filename: MoEx-1_0-st-v1,coreR1,A20080718,MR.cdf
Filesize: 30.53MB
Chip type: MoEx-1_0-st-v1,coreR1,A20080718,MR
RAM: 0.00MB
File format: v4 (binary; XDA)
Dimension: 2560x2560
Number of cells: 6553600
Number of units: 17831
Cells per unit: 367.54
Number of QC units: 1
csR - AffymetrixCelSet$byName(dataSet, chipType=chipType)
print(csR)
AffymetrixCelSet:
Name: Exon Data
Tags:
Path: rawData/Exon Data/MoEx-1_0-st-v1
Platform: Affymetrix
Chip type: MoEx-1_0-st-v1
Number of arrays: 7
Names: DK Litter D15 P1_(MoEx-1_0-st-v1), DK Litter D15
P14_(MoEx-1_0-st-v1), ..., DK Litter D15 P6_(MoEx-1_0-st-v1)
Time period: 2009-06-18 13:22:04 -- 2009-06-30 15:13:54
Total file size: 440.55MB
RAM: 0.01MB
cdf - getCdf(csR)
cdfS - AffymetrixCdfFile$byChipType(getChipType(cdf, fullname=FALSE))
setCdf(csR, cdfS)
bc - GcRmaBackgroundCorrection(csR, type=affinities)
print(bc)
GcRmaBackgroundCorrection:
Data set: Exon Data
Input tags:
User tags: *
Asterisk ('*') tags: GRBC
Output tags: GRBC
Number of files: 7 (440.55MB)
Platform: Affymetrix
Chip type: MoEx-1_0-st-v1
Algorithm parameters: (subsetToUpdate: NULL, typesToUpdate: chr pm,
indicesNegativeControl: NULL, affinities: NULL, type: chr affinities,
opticalAdjust: logi TRUE, gsbAdjust: logi TRUE, gsbParameters: NULL)
Output path: probeData/Exon Data,GRBC/MoEx-1_0-st-v1
Is done: FALSE
RAM: 0.00MB
csB - process(bc, verbose=verbose)
20100927 16:31:40|Background correcting data set...
20100927 16:31:40| Computing probe affinities...
20100927 16:31:40| Computing GCRMA probe affinities for 1257006 units...
20100927 16:31:40| Identify PMs and MMs among the CDF cell indices...
logi [1:5266159] TRUE TRUE TRUE TRUE TRUE TRUE ...
Mode FALSETRUENA's
logical 334476 4931683 0
20100927 16:33:30|MMs are defined as non-PMs
20100927 16:33:30|Number of PMs: 4931683
20100927 16:33:30|Number of MMs: 334476
20100927 16:33:30| Identify PMs and MMs among the CDF cell indices...done
20100927 16:33:30| Reading probe-sequence data...
20100927 16:33:30|Retrieving probe-sequence data...
20100927 16:33:30| Chip type (full): MoEx-1_0-st-v1
20100927 16:33:30| Locating probe-tab file...
20100927 16:33:30| Chip type: MoEx-1_0-st-v1
Error in list(`process(bc, verbose = verbose)` = environment,
`process.GcRmaBackgroundCorrection(bc, verbose = verbose)` = environment,
:
[2010-09-27 16:33:30] Exception: Found probe-tab file only by means of
deprectated (v1) search rules:
at throw(Exception(...))
at throw.default(Found probe-tab file only by means of deprectated (v1
at throw(Found probe-tab file only by means of deprectated (v1) search
at method(static, ...)
at AffymetrixProbeTabFile$findByChipType(chipType, what = what, ...)
at method(static, ...)
at AffymetrixProbeTabFile$byChipType(chipType = chipType, verbose = les
at getProbeSequenceData.AffymetrixCdfFile(this, safe = safe, verbose =
at getProbeSequenceData(this, safe = safe, verbose = verbose)
at computeAffinities.AffymetrixCdfFile(cdf, paths = probePath, ..., ver
at computeAffinities(cdf, paths = probePath, ..., verbose = less(verbos
at bgAdjustGcrma.AffymetrixCelSet(NA, path = probeData/Exon Data,GRBC/
at bgAdjustGcrma(NA, path = probeData/Exon Data,GRBC/MoEx-1_0-st-v1,
at do.call(bgAdjustGcrma, args = args)
at process.GcRmaBackgroundCorrection(
20100927 16:33:30| Locating probe-tab file...done
20100927 16:33:30|Retrieving probe-sequence data...done
20100927 16:33:30| Reading probe-sequence data...done
20100927 16:33:30| Computing GCRMA probe affinities for 1257006
units...done
20100927 16:33:30| Computing probe affinities...done
20100927 16:33:30|Background correcting data set...done
traceback()
17: throw.Exception(Exception(...))
16: throw(Exception(...))
15: throw.default(Found probe-tab file only by means of deprectated (v1)
search rules: ,
pathname)
14: throw(Found probe-tab file only by means of deprectated (v1) search
rules: ,
pathname)
13: method(static, ...)
12: AffymetrixProbeTabFile$findByChipType(chipType, what = what,
...)
11: method(static, ...)
10: AffymetrixProbeTabFile$byChipType(chipType = chipType, verbose =
less(verbose,
100))
9: getProbeSequenceData.AffymetrixCdfFile(this, safe = safe, verbose =
verbose)
8: getProbeSequenceData(this, safe = safe, verbose = verbose)
7: computeAffinities.AffymetrixCdfFile(cdf, paths = probePath, ...,
verbose = less(verbose))
6: computeAffinities(cdf, paths = probePath, ..., verbose = less(verbose))
5:
Re: [aroma.affymetrix] Help needed regarding GCRMA normalization of exon arrays using aroma.affymetrix.....
Hi,
sorry, my mistake. I missed that you already did this.
You are missing the 'MoEx-1_0-st-v1.probe.tab' annotation data file.
You can download it from Affymetrix and you'll find a link to their
support page via http://www.aroma-project.org/chipTypes/MoEx-1_0-st-v1
. Download it (something like MoEx-1_0-st-v1 Probe Sequences,
tabular format (130 MB, 3/19/08)) and place it in
annotationData/chipTypes/MoEx-1_0-st-v1/. You can verify that it is
correct by trying the following:
library(aroma.affymetrix);
ptf - AffymetrixProbeTabFile$byChipType(MoEx-1_0-st-v1);
ptf
AffymetrixProbeTabFile:
Name: MoEx-1_0-st-v1
Tags:
Full name: MoEx-1_0-st-v1
Pathname: annotationData/chipTypes/MoEx-1_0-st-v1/MoEx-1_0-st-v1.probe.tab
File size: 460.47 MB (482839635 bytes)
RAM: 0.01 MB
Number of data rows: NA
Columns [12]: 'probeID', 'probeSetID', 'probeXPos', 'probeYPos',
'assembly', 'seqname', 'start', 'stop', 'strand', 'probeSequence',
'targetStrandedness', 'category'
Number of text lines: NA
AffymetrixCdfFile:
Path: annotationData/chipTypes/MoEx-1_0-st-v1
Filename: MoEx-1_0-st-v1.cdf
Filesize: 274.30MB
Chip type: MoEx-1_0-st-v1
RAM: 0.00MB
File format: v4 (binary; XDA)
Dimension: 2560x2560
Number of cells: 6553600
Number of units: 1257006
Cells per unit: 5.21
Number of QC units: 0
If you get that to work, then your script should work.
Let me now if this solved your problem.
/Henrik
On Mon, Sep 27, 2010 at 1:58 PM, Prithish Banerjee
prithish.baner...@gmail.com wrote:
Respected Dr Bengtsson,
My codes and outputs are as follows:
source(http://aroma-project.org/hbLite.R;);
hbInstall(aroma.affymetrix)
source(http://aroma-project.org/hbLite.R;);
hbInstall(aroma.cn)
verbose - Arguments$getVerbose(-10, timestamp=TRUE);
dataSet - Exon Data
chipType - MoEx-1_0-st-v1
cdf - AffymetrixCdfFile$byChipType(chipType,tags=coreR1,A20080718,MR)
print(cdf)
AffymetrixCdfFile:
Path: annotationData/chipTypes/MoEx-1_0-st-v1
Filename: MoEx-1_0-st-v1,coreR1,A20080718,MR.cdf
Filesize: 30.53MB
Chip type: MoEx-1_0-st-v1,coreR1,A20080718,MR
RAM: 0.00MB
File format: v4 (binary; XDA)
Dimension: 2560x2560
Number of cells: 6553600
Number of units: 17831
Cells per unit: 367.54
Number of QC units: 1
csR - AffymetrixCelSet$byName(dataSet, chipType=chipType)
print(csR)
AffymetrixCelSet:
Name: Exon Data
Tags:
Path: rawData/Exon Data/MoEx-1_0-st-v1
Platform: Affymetrix
Chip type: MoEx-1_0-st-v1
Number of arrays: 7
Names: DK Litter D15 P1_(MoEx-1_0-st-v1), DK Litter D15
P14_(MoEx-1_0-st-v1), ..., DK Litter D15 P6_(MoEx-1_0-st-v1)
Time period: 2009-06-18 13:22:04 -- 2009-06-30 15:13:54
Total file size: 440.55MB
RAM: 0.01MB
cdf - getCdf(csR)
cdfS - AffymetrixCdfFile$byChipType(getChipType(cdf, fullname=FALSE))
setCdf(csR, cdfS)
bc - GcRmaBackgroundCorrection(csR, type=affinities)
print(bc)
GcRmaBackgroundCorrection:
Data set: Exon Data
Input tags:
User tags: *
Asterisk ('*') tags: GRBC
Output tags: GRBC
Number of files: 7 (440.55MB)
Platform: Affymetrix
Chip type: MoEx-1_0-st-v1
Algorithm parameters: (subsetToUpdate: NULL, typesToUpdate: chr pm,
indicesNegativeControl: NULL, affinities: NULL, type: chr affinities,
opticalAdjust: logi TRUE, gsbAdjust: logi TRUE, gsbParameters: NULL)
Output path: probeData/Exon Data,GRBC/MoEx-1_0-st-v1
Is done: FALSE
RAM: 0.00MB
csB - process(bc, verbose=verbose)
20100927 16:31:40|Background correcting data set...
20100927 16:31:40| Computing probe affinities...
20100927 16:31:40| Computing GCRMA probe affinities for 1257006 units...
20100927 16:31:40| Identify PMs and MMs among the CDF cell indices...
logi [1:5266159] TRUE TRUE TRUE TRUE TRUE TRUE ...
Mode FALSE TRUE NA's
logical 334476 4931683 0
20100927 16:33:30| MMs are defined as non-PMs
20100927 16:33:30| Number of PMs: 4931683
20100927 16:33:30| Number of MMs: 334476
20100927 16:33:30| Identify PMs and MMs among the CDF cell indices...done
20100927 16:33:30| Reading probe-sequence data...
20100927 16:33:30| Retrieving probe-sequence data...
20100927 16:33:30| Chip type (full): MoEx-1_0-st-v1
20100927 16:33:30| Locating probe-tab file...
20100927 16:33:30| Chip type: MoEx-1_0-st-v1
Error in list(`process(bc, verbose = verbose)` = environment,
`process.GcRmaBackgroundCorrection(bc, verbose = verbose)` = environment,
:
[2010-09-27 16:33:30] Exception: Found probe-tab file only by means of
deprectated (v1) search rules:
at throw(Exception(...))
at throw.default(Found probe-tab file only by means of deprectated (v1
at throw(Found probe-tab file only by means of deprectated (v1) search
at method(static, ...)
at AffymetrixProbeTabFile$findByChipType(chipType, what = what, ...)
at method(static, ...)
at AffymetrixProbeTabFile$byChipType(chipType = chipType, verbose = les
at getProbeSequenceData.AffymetrixCdfFile(this, safe = safe, verbose =
at getProbeSequenceData(this, safe = safe, verbose = verbose)
at
Re: [aroma.affymetrix] Help needed regarding GCRMA normalization of exon arrays using aroma.affymetrix.....
Hi,
first of all, for this chip type you need to specify:
bc - GcRmaBackgroundCorrection(csR, type=affinities);
Moreover, you cannot use the custom CDF in the
GcRmaBackgroundCorrection step, and have to do the follow workaround
illustrated in the below example:
library(aroma.affymetrix);
verbose - Arguments$getVerbose(-10, timestamp=TRUE);
dataSet - Affymetrix-Tissues;
chipType - MoEx-1_0-st-v1;
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
# Setup data set
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
cdf - AffymetrixCdfFile$byChipType(chipType, tags=coreR1,A20080718,MR);
print(cdf);
csR - AffymetrixCelSet$byName(dataSet, chipType=chipType);
print(csR);
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
# gcRMA-style background correction
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
# Currently, you must use the standard CDF file.
cdf - getCdf(csR);
cdfS - AffymetrixCdfFile$byChipType(getChipType(cdf, fullname=FALSE));
setCdf(csR, cdfS);
bc - GcRmaBackgroundCorrection(csR, type=affinities);
print(bc);
csB - process(bc, verbose=verbose);
print(csB);
# Now, use the custom CDF in what follows
setCdf(csB, cdf);
print(csB);
Yes, those last steps are rather confusing - we're working on updating
the code so you don't have to do that yourself.
FYI, the above solution/workaround was resolved in thread 'GCRMA
normalization with MoEx-1_0-st-v1' of March 24-April 8, 2010, cf.
http://goo.gl/cniq.
Hope this helps
/Henrik
On Fri, Sep 24, 2010 at 2:30 PM, Prithish Banerjee
prithish.baner...@gmail.com wrote:
Hi All,
I am trying to normalize a mouse exon array dataset using GCRMA
normalization technique. I have exactly followed all the necessary steps for
storing the dataset and the cdf file. the code and the output I am using are
as follows:
source(http://aroma-project.org/hbLite.R;);
hbInstall(aroma.affymetrix)
source(http://aroma-project.org/hbLite.R;);
hbInstall(aroma.cn)
verbose - Arguments$getVerbose(-10, timestamp=TRUE);
dataSet - Exon Data [the path in the working directory is rawData/Exon
Data/MoEx-1_0-st-v1/*.CEL files]
chipType - MoEx-1_0-st-v1 [the path in the working directory is
annotationData/chipTypes/MoEx-1_0-st-v1/MoEx-1_0-st-v1,coreR1,A20080718,MR.cdf]
cdf - AffymetrixCdfFile$byChipType(chipType,tags=coreR1,A20080718,MR)
[converted to binary using convertCdf command]
print(cdf)
AffymetrixCdfFile:
Path: annotationData/chipTypes/MoEx-1_0-st-v1
Filename: MoEx-1_0-st-v1,coreR1,A20080718,MR.cdf
Filesize: 30.53MB
Chip type: MoEx-1_0-st-v1,coreR1,A20080718,MR
RAM: 0.00MB
File format: v4 (binary; XDA)
Dimension: 2560x2560
Number of cells: 6553600
Number of units: 17831
Cells per unit: 367.54
Number of QC units: 1
csR - AffymetrixCelSet$byName(dataSet, chipType=chipType)
print(csR)
AffymetrixCelSet:
Name: Exon Data
Tags:
Path: rawData/Exon Data/MoEx-1_0-st-v1
Platform: Affymetrix
Chip type: MoEx-1_0-st-v1
Number of arrays: 7
Names: DK Litter D15 P1_(MoEx-1_0-st-v1), DK Litter D15
P14_(MoEx-1_0-st-v1), ..., DK Litter D15 P6_(MoEx-1_0-st-v1)
Time period: 2009-06-18 13:22:04 -- 2009-06-30 15:13:54
Total file size: 440.55MB
RAM: 0.01MB
cdf - getCdf(csR)
cdfS - AffymetrixCdfFile$byChipType(getChipType(cdf, fullname=FALSE))
setCdf(csR, cdfS)
bc - GcRmaBackgroundCorrection(csR, type=affinities)
print(bc)
GcRmaBackgroundCorrection:
Data set: Exon Data
Input tags:
User tags: *
Asterisk ('*') tags: GRBC
Output tags: GRBC
Number of files: 7 (440.55MB)
Platform: Affymetrix
Chip type: MoEx-1_0-st-v1
Algorithm parameters: (subsetToUpdate: NULL, typesToUpdate: chr pm,
indicesNegativeControl: NULL, affinities: NULL, type: chr affinities,
opticalAdjust: logi TRUE, gsbAdjust: logi TRUE, gsbParameters: NULL)
Output path: probeData/Exon Data,GRBC/MoEx-1_0-st-v1
Is done: FALSE
RAM: 0.00MB
csB - process(bc, verbose=verbose)
20100923 13:24:12|Background correcting data set...
20100923 13:24:12| Computing probe affinities...
20100923 13:24:12| Computing GCRMA probe affinities for 1257006 units...
20100923 13:24:12| Identify PMs and MMs among the CDF cell indices...
logi [1:5266159] TRUE TRUE TRUE TRUE TRUE TRUE ...
Mode FALSE TRUE NA's
logical 334476 4931683 0
20100923 13:25:57| MMs are defined as non-PMs
20100923 13:25:57| Number of PMs: 4931683
20100923 13:25:57| Number of MMs: 334476
20100923 13:25:57| Identify PMs and MMs among the CDF cell indices...done
20100923 13:25:57| Reading probe-sequence data...
20100923 13:25:57| Retrieving probe-sequence data...
20100923 13:25:57| Chip type (full): MoEx-1_0-st-v1
20100923 13:25:57| Locating probe-tab file...
20100923 13:25:57| Chip type: MoEx-1_0-st-v1
Error in list(`process(bc, verbose = verbose)` = environment,
`process.GcRmaBackgroundCorrection(bc, verbose = verbose)` = environment,
:
[2010-09-23
[aroma.affymetrix] Help needed regarding GCRMA normalization of exon arrays using aroma.affymetrix.....
Hi All,
I am trying to normalize a mouse exon array dataset using GCRMA
normalization technique. I have exactly followed all the necessary steps for
storing the dataset and the cdf file. the code and the output I am using are
as follows:
source(http://aroma-project.org/hbLite.R;);
hbInstall(aroma.affymetrix)
source(http://aroma-project.org/hbLite.R;);
hbInstall(aroma.cn)
verbose - Arguments$getVerbose(-10, timestamp=TRUE);
dataSet - Exon Data [the path in the working directory is rawData/Exon
Data/MoEx-1_0-st-v1/*.CEL files]
chipType - MoEx-1_0-st-v1 [the path in the working directory is
annotationData/chipTypes/MoEx-1_0-st-v1/MoEx-1_0-st-v1,coreR1,A20080718,MR.cdf]
cdf - AffymetrixCdfFile$byChipType(chipType,tags=coreR1,A20080718,MR)
[converted to binary using convertCdf command]
print(cdf)
AffymetrixCdfFile:
Path: annotationData/chipTypes/MoEx-1_0-st-v1
Filename: MoEx-1_0-st-v1,coreR1,A20080718,MR.cdf
Filesize: 30.53MB
Chip type: MoEx-1_0-st-v1,coreR1,A20080718,MR
RAM: 0.00MB
File format: v4 (binary; XDA)
Dimension: 2560x2560
Number of cells: 6553600
Number of units: 17831
Cells per unit: 367.54
Number of QC units: 1
csR - AffymetrixCelSet$byName(dataSet, chipType=chipType)
print(csR)
AffymetrixCelSet:
Name: Exon Data
Tags:
Path: rawData/Exon Data/MoEx-1_0-st-v1
Platform: Affymetrix
Chip type: MoEx-1_0-st-v1
Number of arrays: 7
Names: DK Litter D15 P1_(MoEx-1_0-st-v1), DK Litter D15
P14_(MoEx-1_0-st-v1), ..., DK Litter D15 P6_(MoEx-1_0-st-v1)
Time period: 2009-06-18 13:22:04 -- 2009-06-30 15:13:54
Total file size: 440.55MB
RAM: 0.01MB
cdf - getCdf(csR)
cdfS - AffymetrixCdfFile$byChipType(getChipType(cdf, fullname=FALSE))
setCdf(csR, cdfS)
bc - GcRmaBackgroundCorrection(csR, type=affinities)
print(bc)
GcRmaBackgroundCorrection:
Data set: Exon Data
Input tags:
User tags: *
Asterisk ('*') tags: GRBC
Output tags: GRBC
Number of files: 7 (440.55MB)
Platform: Affymetrix
Chip type: MoEx-1_0-st-v1
Algorithm parameters: (subsetToUpdate: NULL, typesToUpdate: chr pm,
indicesNegativeControl: NULL, affinities: NULL, type: chr affinities,
opticalAdjust: logi TRUE, gsbAdjust: logi TRUE, gsbParameters: NULL)
Output path: probeData/Exon Data,GRBC/MoEx-1_0-st-v1
Is done: FALSE
RAM: 0.00MB
csB - process(bc, verbose=verbose)
20100923 13:24:12|Background correcting data set...
20100923 13:24:12| Computing probe affinities...
20100923 13:24:12| Computing GCRMA probe affinities for 1257006 units...
20100923 13:24:12| Identify PMs and MMs among the CDF cell indices...
logi [1:5266159] TRUE TRUE TRUE TRUE TRUE TRUE ...
Mode FALSETRUENA's
logical 334476 4931683 0
20100923 13:25:57|MMs are defined as non-PMs
20100923 13:25:57|Number of PMs: 4931683
20100923 13:25:57|Number of MMs: 334476
20100923 13:25:57| Identify PMs and MMs among the CDF cell indices...done
20100923 13:25:57| Reading probe-sequence data...
20100923 13:25:57|Retrieving probe-sequence data...
20100923 13:25:57| Chip type (full): MoEx-1_0-st-v1
20100923 13:25:57| Locating probe-tab file...
20100923 13:25:57| Chip type: MoEx-1_0-st-v1
Error in list(`process(bc, verbose = verbose)` = environment,
`process.GcRmaBackgroundCorrection(bc, verbose = verbose)` = environment,
:
[2010-09-23 13:25:57] Exception: Found probe-tab file only by means of
deprectated (v1) search rules:
at throw(Exception(...))
at throw.default(Found probe-tab file only by means of deprectated (v1
at throw(Found probe-tab file only by means of deprectated (v1) search
at method(static, ...)
at AffymetrixProbeTabFile$findByChipType(chipType, what = what, ...)
at method(static, ...)
at AffymetrixProbeTabFile$byChipType(chipType = chipType, verbose = les
at getProbeSequenceData.AffymetrixCdfFile(this, safe = safe, verbose =
at getProbeSequenceData(this, safe = safe, verbose = verbose)
at computeAffinities.AffymetrixCdfFile(cdf, paths = probePath, ..., ver
at computeAffinities(cdf, paths = probePath, ..., verbose = less(verbos
at bgAdjustGcrma.AffymetrixCelSet(NA, path = probeData/Exon Data,GRBC/
at bgAdjustGcrma(NA, path = probeData/Exon Data,GRBC/MoEx-1_0-st-v1,
at do.call(bgAdjustGcrma, args = args)
at process.GcRmaBackgroundCorrection(
20100923 13:25:57| Locating probe-tab file...done
20100923 13:25:57|Retrieving probe-sequence data...done
20100923 13:25:57| Reading probe-sequence data...done
20100923 13:25:57| Computing GCRMA probe affinities for 1257006
units...done
20100923 13:25:57| Computing probe affinities...done
20100923 13:25:57|Background correcting data set...done
Could anyone please enlighten me with the type of the error? I will be
highly obliged if anyone please help me with this problem.
Thank you.
Prithish Banerjee.
--
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
[aroma.affymetrix] Help needed regarding GCRMA normalization of exon arrays using aroma.affymetrix.....
Hi All,
I am trying to normalize a mouse exon array dataset using GCRMA
normalization technique. I have exactly followed all the necessary steps for
storing the dataset and the cdf file. the code and the output I am using are
as follows:
source(http://aroma-project.org/hbLite.R;);
hbInstall(aroma.affymetrix)
source(http://aroma-project.org/hbLite.R;);
hbInstall(aroma.cn)
verbose - Arguments$getVerbose(-10, timestamp=TRUE);
dataSet - Exon Data [the path in the working directory is rawData/Exon
Data/MoEx-1_0-st-v1/*.CEL files]
chipType - MoEx-1_0-st-v1 [the path in the working directory is
annotationData/chipTypes/MoEx-1_0-st-v1/MoEx-1_0-st-v1,coreR1,A20080718,MR.cdf]
cdf - AffymetrixCdfFile$byChipType(chipType,tags=coreR1,A20080718,MR)
[converted to binary using convertCdf command]
print(cdf)
AffymetrixCdfFile:
Path: annotationData/chipTypes/MoEx-1_0-st-v1
Filename: MoEx-1_0-st-v1,coreR1,A20080718,MR.cdf
Filesize: 30.53MB
Chip type: MoEx-1_0-st-v1,coreR1,A20080718,MR
RAM: 0.00MB
File format: v4 (binary; XDA)
Dimension: 2560x2560
Number of cells: 6553600
Number of units: 17831
Cells per unit: 367.54
Number of QC units: 1
csR - AffymetrixCelSet$byName(dataSet, chipType=chipType)
print(csR)
AffymetrixCelSet:
Name: Exon Data
Tags:
Path: rawData/Exon Data/MoEx-1_0-st-v1
Platform: Affymetrix
Chip type: MoEx-1_0-st-v1
Number of arrays: 7
Names: DK Litter D15 P1_(MoEx-1_0-st-v1), DK Litter D15
P14_(MoEx-1_0-st-v1), ..., DK Litter D15 P6_(MoEx-1_0-st-v1)
Time period: 2009-06-18 13:22:04 -- 2009-06-30 15:13:54
Total file size: 440.55MB
RAM: 0.01MB
cdf - getCdf(csR)
cdfS - AffymetrixCdfFile$byChipType(getChipType(cdf, fullname=FALSE))
setCdf(csR, cdfS)
bc - GcRmaBackgroundCorrection(csR, type=affinities)
print(bc)
GcRmaBackgroundCorrection:
Data set: Exon Data
Input tags:
User tags: *
Asterisk ('*') tags: GRBC
Output tags: GRBC
Number of files: 7 (440.55MB)
Platform: Affymetrix
Chip type: MoEx-1_0-st-v1
Algorithm parameters: (subsetToUpdate: NULL, typesToUpdate: chr pm,
indicesNegativeControl: NULL, affinities: NULL, type: chr affinities,
opticalAdjust: logi TRUE, gsbAdjust: logi TRUE, gsbParameters: NULL)
Output path: probeData/Exon Data,GRBC/MoEx-1_0-st-v1
Is done: FALSE
RAM: 0.00MB
csB - process(bc, verbose=verbose)
20100923 13:24:12|Background correcting data set...
20100923 13:24:12| Computing probe affinities...
20100923 13:24:12| Computing GCRMA probe affinities for 1257006 units...
20100923 13:24:12| Identify PMs and MMs among the CDF cell indices...
logi [1:5266159] TRUE TRUE TRUE TRUE TRUE TRUE ...
Mode FALSETRUENA's
logical 334476 4931683 0
20100923 13:25:57|MMs are defined as non-PMs
20100923 13:25:57|Number of PMs: 4931683
20100923 13:25:57|Number of MMs: 334476
20100923 13:25:57| Identify PMs and MMs among the CDF cell indices...done
20100923 13:25:57| Reading probe-sequence data...
20100923 13:25:57|Retrieving probe-sequence data...
20100923 13:25:57| Chip type (full): MoEx-1_0-st-v1
20100923 13:25:57| Locating probe-tab file...
20100923 13:25:57| Chip type: MoEx-1_0-st-v1
Error in list(`process(bc, verbose = verbose)` = environment,
`process.GcRmaBackgroundCorrection(bc, verbose = verbose)` = environment,
:
[2010-09-23 13:25:57] Exception: Found probe-tab file only by means of
deprectated (v1) search rules:
at throw(Exception(...))
at throw.default(Found probe-tab file only by means of deprectated (v1
at throw(Found probe-tab file only by means of deprectated (v1) search
at method(static, ...)
at AffymetrixProbeTabFile$findByChipType(chipType, what = what, ...)
at method(static, ...)
at AffymetrixProbeTabFile$byChipType(chipType = chipType, verbose = les
at getProbeSequenceData.AffymetrixCdfFile(this, safe = safe, verbose =
at getProbeSequenceData(this, safe = safe, verbose = verbose)
at computeAffinities.AffymetrixCdfFile(cdf, paths = probePath, ..., ver
at computeAffinities(cdf, paths = probePath, ..., verbose = less(verbos
at bgAdjustGcrma.AffymetrixCelSet(NA, path = probeData/Exon Data,GRBC/
at bgAdjustGcrma(NA, path = probeData/Exon Data,GRBC/MoEx-1_0-st-v1,
at do.call(bgAdjustGcrma, args = args)
at process.GcRmaBackgroundCorrection(
20100923 13:25:57| Locating probe-tab file...done
20100923 13:25:57|Retrieving probe-sequence data...done
20100923 13:25:57| Reading probe-sequence data...done
20100923 13:25:57| Computing GCRMA probe affinities for 1257006
units...done
20100923 13:25:57| Computing probe affinities...done
20100923 13:25:57|Background correcting data set...done
Could anyone please enlighten me with the type of the error? I will be
highly obliged if anyone please help me with this problem.
Thank you.
Prithish Banerjee.
--
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
