Hi,
I try to analyze a tiling array data as stated in the Vignette: MAT -
Tiling array analysis (Promoter 1.0R) (according to
http://www.aroma-project.org).
When running
csN <- process(mn, verbose=verbose, na.rm = TRUE)
an error occurs, saying Error: Argument 'cells' contains 1 NA value(s).
> csN <- process(mn, verbose=verbose, na.rm = TRUE)
20130116 17:18:55|Normalization data set for probe-sequence effects...
20130116 17:18:55| Locating probe-sequence annotation data...
20130116 17:18:55| Getting AromaCellSequenceFile...
20130116 17:18:55| Locating...
20130116 17:18:55| Chip type: Hs_PromPR_v02
20130116 17:18:55| Number of cells: 4691556
20130116 17:18:55| Locating AromaCellSequenceFile...
20130116 17:18:56| Located file:
annotationData/chipTypes/Hs_PromPR_v02/Hs_PromPR_v02.acs
20130116 17:18:56| Locating AromaCellSequenceFile...done
20130116 17:18:56| Locating...done
AromaCellSequenceFile:
Name: Hs_PromPR_v02
Tags:
Full name: Hs_PromPR_v02
Pathname: annotationData/chipTypes/Hs_PromPR_v02/Hs_PromPR_v02.acs
File size: 116.33 MB (121980713 bytes)
RAM: 0.00 MB
Number of data rows: 4691556
File format: v1
Dimensions: 4691556x26
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>20130116 13:24:14
CET</createdOn><platform>Affymetrix</platform><chipType>Hs_PromPR_v02</chipType>
Chip type: Hs_PromPR_v02
Platform: Affymetrix
20130116 17:18:56| Getting AromaCellSequenceFile...done
20130116 17:18:56| Locating probe-sequence annotation data...done
20130116 17:18:56| Locating match scores annotation data...
20130116 17:18:56| Locating AromaCellMatchScoreFile...
20130116 17:18:56| Located file:
annotationData/chipTypes/Hs_PromPR_v02/Hs_PromPR_v02.acm
AromaCellMatchScoreFile:
Name: Hs_PromPR_v02
Tags:
Full name: Hs_PromPR_v02
Pathname: annotationData/chipTypes/Hs_PromPR_v02/Hs_PromPR_v02.acm
File size: 4.47 MB (4691738 bytes)
RAM: 0.00 MB
Number of data rows: 4691556
File format: v1
Dimensions: 4691556x1
Column classes: integer
Number of bytes per column: 1
Footer: <createdOn>20130116 13:50:13
CET</createdOn><platform>Affymetrix</platform><chipType>Hs_PromPR_v02</chipType>
Chip type: Hs_PromPR_v02
Platform: Affymetrix
20130116 17:18:56| Locating AromaCellMatchScoreFile...done
20130116 17:18:56| Locating match scores annotation data...done
20130116 17:18:56| Reading 'non-missing' cells to fit...
20130116 17:18:56| Cells to fit:
int(0)
20130116 17:18:56| Reading 'non-missing' cells to fit...done
20130116 17:18:56| Normalizing 128 arrays...
20130116 17:18:56| Path: probeData/IFB_128samples,MN,lm/Hs_PromPR_v02...
20130116 17:18:56| Number cells per chunk: 1000001
20130116 17:18:56| Fitting chunk #1 of 0...
20130116 17:18:56| Cells:
int NA
20130116 17:18:56| Reading design matrix...
20130116 17:18:56| Retrieving design matrix...
20130116 17:18:56| Cells:
int NA
20130116 17:18:56| Locating probe-sequence annotation data...
20130116 17:18:56| Getting AromaCellSequenceFile...
AromaCellSequenceFile:
Name: Hs_PromPR_v02
Tags:
Full name: Hs_PromPR_v02
Pathname: annotationData/chipTypes/Hs_PromPR_v02/Hs_PromPR_v02.acs
File size: 116.33 MB (121980713 bytes)
RAM: 0.00 MB
Number of data rows: 4691556
File format: v1
Dimensions: 4691556x26
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>20130116 13:24:14
CET</createdOn><platform>Affymetrix</platform><chipType>Hs_PromPR_v02</chipType>
Chip type: Hs_PromPR_v02
Platform: Affymetrix
20130116 17:18:57| Getting AromaCellSequenceFile...done
20130116 17:18:57| Locating probe-sequence annotation data...done
20130116 17:18:57| Locating match scores annotation data...
20130116 17:18:57| Locating match scores annotation data...done
20130116 17:18:57| Reading sequence matrix...
[2013-01-16 17:18:57] Exception: Argument 'cells' contains 1 NA value(s).
at #13. getNumerics.Arguments(static, ..., asMode = "integer", disallow =
disallow)
- getNumerics.Arguments() is in environment 'R.utils'
at #12. getNumerics(static, ..., asMode = "integer", disallow = disallow)
- getNumerics() is in environment 'R.utils'
at #11. getIntegers.Arguments(static, x, ..., range = range, .name =
.name)
- getIntegers.Arguments() is in environment 'R.utils'
at #10. getIntegers(static, x, ..., range = range, .name = .name)
- getIntegers() is in environment 'R.utils'
at #09. getIndices.Arguments(static, ...)
- getIndices.Arguments() is in environment 'R.utils'
at #08. getIndices(static, ...)
- getIndices() is in environment 'R.utils'
at #07. Arguments$getIndices(cells, max = nbrOfCells)
- Arguments$getIndices() is local of the calling function
at #06. readSequenceMatrix.AromaCellSequenceFile(aps, cells = cells,
verbose = verbose)
- readSequenceMatrix.AromaCellSequenceFile() is in environment
'aroma.core'
at #05. readSequenceMatrix(aps, cells = cells, verbose = verbose)
- readSequenceMatrix() is in environment 'aroma.core'
at #04. getDesignMatrix.MatNormalization(this, cells = cellsToFit[cc],
verbose = verbose)
- getDesignMatrix.MatNormalization() is in environment
'aroma.affymetrix'
at #03. getDesignMatrix(this, cells = cellsToFit[cc], verbose = verbose)
- getDesignMatrix() is in environment 'aroma.affymetrix'
at #02. process.MatNormalization(mn, verbose = verbose, na.rm = TRUE)
- process.MatNormalization() is in environment 'aroma.affymetrix'
at #01. process(mn, verbose = verbose, na.rm = TRUE)
- process() is in environment 'aroma.core'
Error: Argument 'cells' contains 1 NA value(s).
20130116 17:18:57| Reading sequence matrix...done
20130116 17:18:57| Retrieving design matrix...done
20130116 17:18:57| Reading design matrix...done
20130116 17:18:57| Fitting chunk #1 of 0...done
20130116 17:18:57| Path:
probeData/IFB_128samples,MN,lm/Hs_PromPR_v02...done
20130116 17:18:57| Normalizing 128 arrays...done
20130116 17:18:57|Normalization data set for probe-sequence effects...done
I did the same analysis before for a smaller dataset and it all went fine.
The only difference now is that i'm creating the cdf file and all
associated files from the appropriate BpMap file (according to the "How-to"
manual on http://www.aroma-project.org).
I'm using the latest version of aroma package (aroma.affymetrix_2.8.0) and
cdf looks like this:
> print(cdf)
AffymetrixCdfFile:
Path:
annotationData/chipTypes/Hs_PromPR_v02/annotationData/chipTypes/Hs_PromPR_v02
Filename: Hs_PromPR_v02.cdf
Filesize: 60.30MB
Chip type: Hs_PromPR_v02
RAM: 0.18MB
File format: v4 (binary; XDA)
Dimension: 2166x2166
Number of cells: 4691556
Number of units: 22405
Cells per unit: 209.40
Number of QC units: 0
Does anybody know whats the problem?
Thanks for any help!
--
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