Error in strsplit(header, split = "\n") : non-character argument

[Holger.Trucks]

Hi,

I have a little problem doing the allelic crosstalk calibration, maybe
someone can help me out with this?

regards
Holger

**********
[...]
20100118 12:02:44| Storing calibrated data...
20100118 12:02:44| Creating CEL file for results, if missing...
20100118 12:02:44| Creating CEL file...
20100118 12:02:44| Chip type: GenomeWideSNP_6,Full
20100118 12:02:44| Pathname: probeData/CBE,ACC,ra,-XY/
GenomeWideSNP_6/CBE_CAE_1005_270508_GWS6.CEL
20100118 12:02:44| Method 'copy'...
20100118 12:02:44| Copying file...
20100118 12:02:44| Copying file...done
20100118 12:02:44| Renaming AffymetrixCelFile pathname...
20100118 12:02:44| Source: probeData/CBE,ACC,ra,-XY/
GenomeWideSNP_6/CBE_CAE_1005_270508_GWS6.CEL.tmp
20100118 12:02:44| Destination: probeData/CBE,ACC,ra,-XY/
GenomeWideSNP_6/CBE_CAE_1005_270508_GWS6.CEL
20100118 12:02:44| Renaming file...
20100118 12:02:44| Renaming file...done
20100118 12:02:44| Renaming AffymetrixCelFile pathname...done
20100118 12:02:44| Method 'copy'...done
Fehler in strsplit(header, split = "\n") : Nicht-Charakter Argument #
Error in strsplit(header, split = "\n") : Non-character argument
20100118 12:02:45| Creating CEL file...done
20100118 12:02:45| Creating CEL file for results, if missing...done
20100118 12:02:45| Storing calibrated data...done
20100118 12:02:45| Array #1 ('CBE_CAE_1005_270508_GWS6') of
908...done
20100118 12:02:45| Calibrating 908 arrays...done
20100118 12:02:45|Calibrating data set for allelic cross talk...done
> csC
Fehler: Objekt 'csC' nicht gefunden # Error: Object 'csC' not found
>
> sessionInfo()
R version 2.9.0 Under development (unstable) (2009-02-10 r47895)
x86_64-unknown-linux-gnu

locale:
LC_CTYPE=de_DE;LC_NUMERIC=C;LC_TIME=de_DE;LC_COLLATE=de_DE;LC_MONETARY=C;LC_MESSAGES=de_DE;LC_PAPER=de_DE;LC_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=de_DE;LC_IDENTIFICATION=C

attached base packages:
[1] stats graphics grDevices utils datasets methods base

other attached packages:
[1] sfit_0.1.8 aroma.affymetrix_1.4.0 aroma.apd_0.1.7
[4] affxparser_1.16.0 R.huge_0.2.0 aroma.core_1.4.0
[7] aroma.light_1.15.1 matrixStats_0.1.8 R.rsp_0.3.6
[10] R.filesets_0.7.0 digest_0.4.2 R.cache_0.2.0
[13] R.utils_1.3.0 R.oo_1.6.6 R.methodsS3_1.1.0

[Henrik Bengtsson]

Hi,

some requests for troubleshooting:

1. Please provide your full script (at least until the point where you
get the error).

2. What does traceback() report immediately after you get the error?

3. A corrupt CEL file? Show the details of the first CEL file, e.g.
print(getFile(csR,1)).

4. Try to drop the first file and see if it works with the others, e.g.

csR <- extract(csR, -1);
acc <- AllelicCrosstalkCalibration(csR, model="CRMAv2");
csC <- process(acc, verbose=verbose);

/Henrik

> --
> 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.
>
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[Holger.Trucks]

OK, I tried some of your suggestions and now it seems that the error
(Error in strsplit(header, split = "\n") : Non-character argument)
occurs already during defining the Cel-files.
(dropping the first file does not work, maybe it is a general problem
of the CEL files?)
I did a test-run some time ago with windows (with only a few CEL-
files), there I experienced no errors.

**************
> cs <- AffymetrixCelSet$byName("CBE", cdf=cdf)
> cs
AffymetrixCelSet:
Name: CBE
Tags:
Path: rawData/CBE/GenomeWideSNP_6
Platform: Affymetrix
Chip type: GenomeWideSNP_6,Full
Number of arrays: 907
Names: CBE_CAE_103oA_150508_GWS6, CBE_CAE_111oA_060508_GWS6, ...,
CBE_CAE_W760_090508_GWS6
Time period: [not reported if more than 500 arrays]
Total file size: 59706.02MB
RAM: 1.14MB
> print(getFile(cs,1))

Fehler in strsplit(header, split = "\n") : Nicht-Charakter Argument
# Error in strsplit(header, split = "\n") : Non-character argument

> traceback()
12: strsplit(header, split = "\n")
11: unlist(strsplit(header, split = "\n"))
10: getHeaderV3.AffymetrixCelFile(this)
9: getHeaderV3(this)
8: getTimestamp.AffymetrixCelFile(this)
7: getTimestamp(this)
6: sprintf("Timestamp: %s", as.character(getTimestamp(this)))
5: as.character.AffymetrixCelFile(x)
4: as.character(x)
3: print(as.character(x))
2: print.Object(getFile(cs, 1))
1: print(getFile(cs, 1))

[Henrik Bengtsson]

Ok,

try to update to affxparser v1.18.0 or newer, cf.

http://bioconductor.org/packages/2.5/bioc/html/affxparser.html

Make sure to restart R. If that works, let me know, because then I
will update the aroma.affymetrix package requirements to be
"affxparser (>= 1.18.0)".

It updating affxparser does not help, what does this output:

cs <- AffymetrixCelSet$byName("CBE", cdf=cdf);
cf <- getFile(cs, 1);
print(getFileFormat(cf));
str(readCelHeader(getPathname(cf)));

/Henrik

> Fehler in strsplit(header, split = "\n") : Nicht-Charakter Argument
> # Error in strsplit(header, split = "\n") : Non-character argument

>> traceback()
> 12: strsplit(header, split = "\n")
> 11: unlist(strsplit(header, split = "\n"))
> 10: getHeaderV3.AffymetrixCelFile(this)
> 9: getHeaderV3(this)
> 8: getTimestamp.AffymetrixCelFile(this)
> 7: getTimestamp(this)
> 6: sprintf("Timestamp: %s", as.character(getTimestamp(this)))
> 5: as.character.AffymetrixCelFile(x)
> 4: as.character(x)
> 3: print(as.character(x))
> 2: print.Object(getFile(cs, 1))
> 1: print(getFile(cs, 1))
>
>

> On 18 Jan., 12:38, Henrik Bengtsson <henrik.bengts...@gmail.com>

> wrote:
>> Hi,
>>
>> some requests for troubleshooting:
>>
>> 1. Please provide your full script (at least until the point where you
>> get the error).
>>
>> 2. What does traceback() report immediately after you get the error?
>>
>> 3. A corrupt CEL file? Show the details of the first CEL file, e.g.
>> print(getFile(csR,1)).
>>
>> 4. Try to drop the first file and see if it works with the others, e.g.
>>
>> csR <- extract(csR, -1);
>> acc <- AllelicCrosstalkCalibration(csR, model="CRMAv2");
>> csC <- process(acc, verbose=verbose);
>>
>> /Henrik
>>
>> On Mon, Jan 18, 2010 at 3:23 AM, Holger.Trucks
>>

[Holger.Trucks]

Hi,

updating affxparser did not work.

This is the requested output:

> cs <- AffymetrixCelSet$byName("CBE", cdf=cdf);
> cf <- getFile(cs, 1);
> print(getFileFormat(cf));

[1] "v4 (binary; XDA)"
> str(readCelHeader(getPathname(cf)));
List of 12
$ filename : chr "rawData/CBE/GenomeWideSNP_6/
CBE_CAE_1005_270508_GWS6.CEL"
$ version : int 4
$ cols : int 2680
$ rows : int 2572
$ total : int 6892960
$ algorithm : NULL
$ parameters: NULL
$ chiptype : NULL
$ header : NULL
$ cellmargin: int 4
$ noutliers : int 21584
$ nmasked : int 0
>

On 18 Jan., 19:59, Henrik Bengtsson <henrik.bengts...@gmail.com>
wrote:

> Ok,
>
> try to update to affxparser v1.18.0 or newer, cf.
>
>  http://bioconductor.org/packages/2.5/bioc/html/affxparser.html
>
> Make sure to restart R.  If that works, let me know, because then I
> will update the aroma.affymetrix package requirements to be
> "affxparser (>= 1.18.0)".
>
> It updating affxparser does not help, what does this output:
>
> cs <- AffymetrixCelSet$byName("CBE", cdf=cdf);
> cf <- getFile(cs, 1);
> print(getFileFormat(cf));
> str(readCelHeader(getPathname(cf)));
>
> /Henrik
>
> On Mon, Jan 18, 2010 at 5:04 AM, Holger.Trucks
>

[Henrik Bengtsson]

Hi,

this seems to be a non-standard CEL file (ho chiptype, header etc).
If you zip this CEL file and make it available to me for download, I
can have a look it. It would also be useful if you can find out how
(software etc) these files were created in the first place.

/Henrik

[Holger.Trucks]

Hi,

I've send yoou a dowlnoad link from the Cel-file above.
Our arrays have been analysed with Affy GTC3.x and the CEL files were
not changed. Some of our files are directly from Affymetrix, thou they
are not part of this analysis I tested them and it didnt worked
either.

I tried to create the output from above on my windows system, there
everything seems to be OK:

***********************
> cs <- AffymetrixCelSet$byName("testor2", cdf=cdf)
> cs
AffymetrixCelSet:
Name: testor2
Tags:
Path: rawData/testor2/GenomeWideSNP_6

Platform: Affymetrix
Chip type: GenomeWideSNP_6,Full

Number of arrays: 1
Names: CBE_CAE_1005_270508_GWS6
Time period: 2008-05-27 15:34:13 -- 2008-05-27 15:34:13
Total file size: 65.82MB
RAM: 0.00MB

> cf <- getFile(cs, 1)
> print(getFileFormat(cf))
[1] "v4 (binary; XDA)"
> str(readCelHeader(getPathname(cf)))
List of 12

$ filename : chr "rawData/testor2/GenomeWideSNP_6/

CBE_CAE_1005_270508_GWS6.CEL"
$ version : int 4
$ cols : int 2680
$ rows : int 2572
$ total : int 6892960

$ algorithm : chr "Percentile"
$ parameters: chr "Percentile:75;CellMargin:4;OutlierHigh:
1.500;OutlierLow:1.004;AlgVersion:
6.0;FixedCellSize:TRUE;FullFeatureWidth:7;FullFeatureH"| __truncated__
$ chiptype : chr "GenomeWideSNP_6"
$ header : chr
"Cols=2680\nRows=2572\nTotalX=2680\nTotalY=2572\nOffsetX=0\nOffsetY=0\nGridCornerUL=641
813\nGridCornerUR=19772 704\nGridCornerL"| __truncated__

$ cellmargin: int 4
$ noutliers : int 21584
$ nmasked : int 0

On 19 Jan., 18:16, Henrik Bengtsson <henrik.bengts...@gmail.com>
wrote:
> Hi,
>

> this seems to be a non-standard CEL file (ho chiptype, header etc).
> If you zip this CEL file and make it available to me for download, I
> can have a look it.  It would also be useful if you can find out how
> (software etc) these files were created in the first place.
>
> /Henrik
>
> On Tue, Jan 19, 2010 at 1:48 AM, Holger.Trucks
>