20 data files should be no problems. I'm still quite sure that you
have '#' in your generated column names. Could you send a file
containing the first 30 rows of the generate
'2012,ACC,ra,-XY,BPN,-XY,AVG,A+B,FLN,-XY,total.txt' file?
/Henrik
On Mon, Mar 5, 2012 at 7:05 PM, Yu Song <ys...@oakland.edu> wrote:
> Dear Henrik,
>
> Thank you for this insight! That's the reason I renamed them and rerun
> the prenormalization, the CBS and then exported the data to the text
> tile, but still I got the same error message as I said in the last
> email(The error message I post was after the rename of the affymetrix
> CEL files).
>
> In general, I run the prenormalization, the CBS and writeDataFrame
> both before and after the changing of the CEL file names, got the same
> error message. It could eliminate the odd of incompatibility of the
> file name. Do you think it might be the problem with too many
> patients(20)?
>
> Thanks a lot for your help!
> Yu
>
> On Mon, Mar 5, 2012 at 2:29 PM, Henrik Bengtsson
> <henrik.bengts...@aroma-project.org> wrote:
>> Hi Yu,
>>
>> the quick answer is that your file has been successfully written, but
>> depending on where you're loading it, the column names may not be
>> correctly parsed. The easy fix is to manually replace all '#'
>> characters with, say, 'No' in the column names of the generated file.
>> Alternatively, you can do the following trick before calling
>> writeDataFrame() to have this done from within R:
>>
>> setFullNamesTranslator(ds, function(names, ...) { gsub("#", "No",
>> names, fixed=TRUE) });
>>
>> More details below...
>>
>> On Sat, Mar 3, 2012 at 8:13 PM, Yu Song <ys...@oakland.edu> wrote:
>>> Hi Henrik,
>>>
>>> Thanks for the help on "Write data as a tab-delimited text file".
>>>
>>> I met a problem when doing "Export all data of a data set to a
>>> tab-delimited text file with annotation data added":
>>>
>>> The error said: "more columns than column names" when I command
>>> writeDataFrame.
>>> The screensnap is attached.
>>> I have 20 patients in files which I doubted the way it named might be
>>> the problem:
>>> ------------------------------------------------------------------------------------
>>> SX0080817D JK 268 Mar 12 2010_(GenomeWideSNP_6),total.asb
>>> SX00808177 MP 303 Mar 12 2010_(GenomeWideSNP_6),total.asb
>>> SX00808174 MW 384 Mar 12 2010_(GenomeWideSNP_6),total.asb
>>> SX0080816E DC 325 Mar 12 2010_(GenomeWideSNP_6),total.asb
>>> SX0080816B DD 383 Mar 23 2010_(GenomeWideSNP_6),total.asb
>>> SX00808168 KA 383 Mar 23 2010_(GenomeWideSNP_6),total.asb
>>> SX00807e37 DK 226 Mar 12 2010_(GenomeWideSNP_6),total.asb
>>> SX00807E2A GJ 7 Mar 12 2010_(GenomeWideSNP_6),total.asb
>>> #9 (work #159) SX00811CFA (01.17.12)_(GenomeWideSNP_6),total.asb
>>> #8 re-do (work #159) SX00811D02 (1.31.12)_(GenomeWideSNP_6),total.asb
>>> #7 re-do (work #159) SX00811CF1 (1.31.12)_(GenomeWideSNP_6),total.asb
>>> #5 (work #159) SX00811CFC (01.17.12)_(GenomeWideSNP_6),total.asb
>>> #4 (work #159) SX00811CFB (01.17.12)_(GenomeWideSNP_6),total.asb
>>> #19(work #159) SX00811CFF (01.17.12)_(GenomeWideSNP_6),total.asb
>>> #18 (work #159) SX008144F8 (01.17.12)_(GenomeWideSNP_6),total.asb
>>> #14 (work #159) SX00811CFE (01.17.12)_(GenomeWideSNP_6),total.asb
>>> #13 (work #159) SX00807DEE (01.17.12)_(GenomeWideSNP_6),total.asb
>>> #12 (work #159) SX008144FE (01.17.12)_(GenomeWideSNP_6),total.asb
>>> #11 (work #159) SX00811CEF (01.17.12)_(GenomeWideSNP_6),total.asb
>>> #1 (work #159) SX00808A11 (01.17.12)_(GenomeWideSNP_6),total.asb
>>> ------------------------------------------------------------------------------------------------------------------------------
>>> I tried modifying the file name in case if aroma is name sensitive.
>>> Then I rerun the prenormalization, the CBS and exportation the data to
>>> text tile, but still I got the same error message:
>>
>> You mean to say *case* sensitive? That would not make difference.
>> More below...
>>
>>>
>>> ------------------------------------------------------------------------------------------------------------------------------
>>>> dsTxt <- writeDataFrame(ds, columns=c("unitName", "chromosome",
>>>> "position", "*"));
>>> Error in list(`writeDataFrame(ds, columns = c("unitName",
>>> "chromosome", "position", "*")` = <environment>, :
>>>
>>> [2012-03-03 23:02:07] Exception: File format error of the tabular file
>>> ('totalAndFracBData,txt/2012,ACC,ra,-XY,BPN,-XY,AVG,A+B,FLN,-XY/GenomeWideSNP_6/2012,ACC,ra,-XY,BPN,-XY,AVG,A+B,FLN,-XY,total.txt'):
>>> more columns than column names
>>> at throw(Exception(...))
>>> at throw.default("File format error of the tabular file ('",
>>> getPathname(thi
>>> at throw("File format error of the tabular file ('", getPathname(this),
>>> "'):
>>> at value[[3]](cond)
>>> at tryCatchOne(expr, names, parentenv, handlers[[1]])
>>> at tryCatchList(expr, classes, parentenv, handlers)
>>> at tryCatch({
>>> at verify.TabularTextFile(this, ..., verbose = verbose)
>>> at verify(this, ..., verbose = verbose)
>>> at TabularTextFile(pathname, sep = sep)
>>> at writeDataFrame.AromaUnitSignalBinarySet(ds, columns = c("unitName",
>>> "chro
>>> at NextMethod("writeDataFrame", this, filename = filename, ...)
>>> at writeDataFrame.AromaUnitTotalCnBinarySet(ds, columns = c("unitName",
>>> "chr
>>> at writeDataFrame(ds, columns = c("unitName", "chromo
>>
>> Reading this stacktrace backwards, the error is generated in
>> TabularTextFile(), which is called by writeDataFrame() [at the very
>> end] to assert that the generated file can be properly parsed by R.
>> Because you have '#' in your filenames, which becomes column names,
>> the assertion test identifies a "conflict" with column names having
>> '#":s and the file header comments starting with '#':s. I've
>> overlooked this use case, and I'll add it to the todo list to either
>> detect & warn about this, or possible make TabularTextFile() smarter
>> about this case.
>>
>> /Henrik
>>
>>> ----------------------------------------------------------------------------------------------------------------
>>
>>
>>>
>>> Thanks a lot!
>>>
>>> Yu
>>>
>>> On Fri, Mar 2, 2012 at 12:07 PM, Henrik Bengtsson
>>> <henrik.bengts...@aroma-project.org> wrote:
>>>> Hi.
>>>>
>>>> On Fri, Mar 2, 2012 at 8:52 AM, Yu Song <ys...@oakland.edu> wrote:
>>>>> Dear Mr.Bengtsson,
>>>>>
>>>>> I am trying to create a data containing the "unitName", "chromosome"
>>>>> and "position" from the output CEL of preprocessing.
>>>>
>>>> What type of CEL files? What type of preprocessing?
>>>>
>>>> /H
>>>>
>>>>> Is there a certain command to do this?
>>>>>
>>>>> Thanks!
>>>>>
>>>>> Yu Song
>>>
>>>
>>>
>>> --
>>> Best regards,
>>> Yu Song
>
>
>
> --
> Best regards,
> Yu Song
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