I managed to reproduce this now:
Error in (...) : 3 arguments passed to '(' which requires 1
20150123 08:48:49| Could not locate monocell CDF. Will create one for chip type.
..done
20150123 08:48:49|Retrieving monocell CDF...done
> traceback()
5: .writeCdfUnits(con = con, srcUnits, verbose = verbose2)
4: createMonocellCdf.AffymetrixCdfFile(this, ..., verbose = less(verbose))
3: createMonocellCdf(this, ..., verbose = less(verbose))
2: getMonocellCdf.AffymetrixCdfFile(cdf, verbose = Arguments$getVerbose(-8,
timestamp = TRUE))
1: getMonocellCdf(cdf, verbose = Arguments$getVerbose(-8, timestamp = TRUE))
I'll investigate and fix this asap.
/Henrik
On Fri, Jan 23, 2015 at 7:37 AM, Henrik Bengtsson <h...@biostat.ucsf.edu> wrote:
>
> On Jan 23, 2015 7:36 AM, "Henrik Bengtsson" <h...@biostat.ucsf.edu> wrote:
>>
>> This is odd for several reasons, e.g. I'm puzzled how you ended up with a
>> monocell CDF previously but now it gives an error. Let's troubleshoot
>> more...
>>
>> What does troubleshoot() output directly after you get that error?
>
> I meant traceback()
>
>>
>> Henrik
>>
>> On Jan 23, 2015 7:23 AM, "Qingzhou Zhang" <zqznept...@gmail.com> wrote:
>> >
>> > Thanks, Henrik,
>> >
>> > It seems that something went wrong with the monocell cdf file by
>> > troubleshooting:
>> >
>> >
>> > > cdf
>> >
>> > AffymetrixCdfFile:
>> >
>> > Path: annotationData/chipTypes/HG-U133_Plus_2
>> >
>> > Filename: HG-U133_Plus_2,monocell.CDF
>> >
>> > File size: 4.88 MB (5116945 bytes)
>> >
>> > Chip type: HG-U133_Plus_2,monocell
>> >
>> > RAM: 0.46MB
>> >
>> > File format: v4 (binary; XDA)
>> >
>> > Dimension: 182x182
>> >
>> > Number of cells: 33124
>> >
>> > Number of units: 27604
>> >
>> > Cells per unit: 1.20
>> >
>> > Number of QC units: 9
>> >
>> >
>> >
>> > So I have deleted the previous monocell cdf file in
>> > annotationData/chipTypes/HG-U133_Plus_2 and re-create it by the following:
>> >
>> > cdf <- AffymetrixCdfFile$byChipType("HG-U133_Plus_2")
>> >
>> > cdfM <- getMonocellCdf(cdf, verbose = Arguments$getVerbose(-8, timestamp
>> > = TRUE))
>> >
>> >
>> >
>> > However, the above process also failed, here is the output:
>> >
>> > > cdfM <- getMonocellCdf(cdf, verbose = Arguments$getVerbose(-8,
>> > > timestamp = TRUE))
>> >
>> > 20150123 21:47:53|Retrieving monocell CDF...
>> >
>> > 20150123 21:47:53| Monocell chip type: HG-U133_Plus_2,monocell
>> >
>> > 20150123 21:47:53| Locating monocell CDF...
>> >
>> > 20150123 21:47:53| Pathname:
>> >
>> > 20150123 21:47:53| Locating monocell CDF...done
>> >
>> > 20150123 21:47:53| Could not locate monocell CDF. Will create one for
>> > chip type...
>> >
>> > 20150123 21:47:53| Creating monocell CDF...
>> >
>> > 20150123 21:47:53| Chip type: HG-U133_Plus_2
>> >
>> > 20150123 21:47:53| Validate (main) CDF...
>> >
>> > 20150123 21:47:54| Validate (main) CDF...done
>> >
>> > 20150123 21:47:55| Adding temporary suffix from file...
>> >
>> > 20150123 21:47:55| Pathname:
>> > annotationData/chipTypes/HG-U133_Plus_2/HG-U133_Plus_2,monocell.CDF
>> >
>> > 20150123 21:47:55| Suffix: .tmp
>> >
>> > 20150123 21:47:55| Rename existing file?: FALSE
>> >
>> > 20150123 21:47:55| Temporary pathname:
>> > annotationData/chipTypes/HG-U133_Plus_2/HG-U133_Plus_2,monocell.CDF.tmp
>> >
>> > 20150123 21:47:55| Adding temporary suffix from file...done
>> >
>> > 20150123 21:47:55| Number of cells per group field: 1
>> >
>> > 20150123 21:47:55| Reading CDF group names...
>> >
>> > 20150123 21:47:55| Reading CDF group names...done
>> >
>> > used (Mb) gc trigger (Mb) max used (Mb)
>> >
>> > Ncells 603933 32.3 899071 48.1 741108 39.6
>> >
>> > Vcells 1027587 7.9 1757946 13.5 1424724 10.9
>> >
>> > used (Mb) gc trigger (Mb) max used (Mb)
>> >
>> > Ncells 549349 29.4 899071 48.1 899071 48.1
>> >
>> > Vcells 945722 7.3 1757946 13.5 1424724 10.9
>> >
>> > 20150123 21:47:56| Number of cells per unit:
>> >
>> > Min. 1st Qu. Median Mean 3rd Qu. Max.
>> >
>> > 1 1 1 1 1 1
>> >
>> > 20150123 21:47:56| Reading CDF QC units...
>> >
>> > 20150123 21:47:56| Reading CDF QC units...done
>> >
>> > 20150123 21:47:56| Number of QC cells: 5385 in 9 QC units (0.1MB)
>> >
>> > 20150123 21:47:56| Total number of cells: 60060
>> >
>> > 20150123 21:47:56| Best array dimension: 246x245 (=60270 cells, i.e.
>> > 210 left-over cells)
>> >
>> > 20150123 21:47:56| Creating CDF header with source CDF as template...
>> >
>> > 20150123 21:47:56| Setting up header...
>> >
>> > 20150123 21:47:56| Reading CDF header...
>> >
>> > 20150123 21:47:56| Reading CDF header...done
>> >
>> > 20150123 21:47:56| Reading CDF unit names...
>> >
>> > 20150123 21:47:56| Reading CDF unit names...done
>> >
>> > 20150123 21:47:56| Setting up header...done
>> >
>> > 20150123 21:47:56| Writing...
>> >
>> > 20150123 21:47:56| destHeader:
>> >
>> > List of 12
>> >
>> > $ ncols : int 245
>> >
>> > $ nrows : int 246
>> >
>> > $ nunits : int 54675
>> >
>> > $ nqcunits : int 9
>> >
>> > $ refseq : chr ""
>> >
>> > $ chiptype : chr "HG-U133_Plus_2"
>> >
>> > $ filename : chr
>> > "annotationData/chipTypes/HG-U133_Plus_2/HG-U133_Plus_2.cdf"
>> >
>> > $ rows : int 1164
>> >
>> > $ cols : int 1164
>> >
>> > $ probesets : int 54675
>> >
>> > $ qcprobesets: int 9
>> >
>> > $ reference : chr ""
>> >
>> > 20150123 21:47:56| unitNames:
>> >
>> > chr [1:54675] "AFFX-BioB-5_at" "AFFX-BioB-M_at" "AFFX-BioB-3_at"
>> > "AFFX-BioC-5_at" ...
>> >
>> > 20150123 21:47:56| qcUnitLengths:
>> >
>> > num [1:9] 15966 174 230 1658 69 ...
>> >
>> > 20150123 21:47:56| unitLengths:
>> >
>> > num [1:54675] 116 116 116 116 116 116 116 116 116 116 ...
>> >
>> > used (Mb) gc trigger (Mb) max used (Mb)
>> >
>> > Ncells 561416 30.0 984024 52.6 899071 48.1
>> >
>> > Vcells 1120064 8.6 1925843 14.7 1515846 11.6
>> >
>> > used (Mb) gc trigger (Mb) max used (Mb)
>> >
>> > Ncells 562232 30.1 984024 52.6 899071 48.1
>> >
>> > Vcells 1010995 7.8 5484388 41.9 6516658 49.8
>> >
>> > 20150123 21:47:57| Writing...done
>> >
>> > 20150123 21:47:57| Creating CDF header with source CDF as
>> > template...done
>> >
>> > 20150123 21:47:57| Writing QC units...
>> >
>> > 20150123 21:47:57| Rearranging QC unit cell indices...
>> >
>> > 20150123 21:47:57| Units: 20150123 21:47:57|
>> >
>> > 20150123 21:47:57| Rearranging QC unit cell indices...done
>> >
>> > used (Mb) gc trigger (Mb) max used (Mb)
>> >
>> > Ncells 562529 30.1 984024 52.6 984024 52.6
>> >
>> > Vcells 994748 7.6 3510008 26.8 6516658 49.8
>> >
>> > 20150123 21:47:57| Writing QC units...done
>> >
>> > 20150123 21:47:57| Number of units: 54675
>> >
>> > 20150123 21:47:57| Argument 'ram': 1.000000
>> >
>> > 20150123 21:47:57| Average unit length: 116.000000 bytes
>> >
>> > 20150123 21:47:57| Number of chunks: 2 (34482 units/chunk)
>> >
>> > 20150123 21:47:57| Reading, extracting, and writing units...
>> >
>> > 20150123 21:47:57| Chunk #1 of 2 (34482 units)
>> >
>> > 20150123 21:47:57| Reading CDF list structure...
>> >
>> > 20150123 21:47:59| Reading CDF list structure...done
>> >
>> > => RAM: 132MB
>> >
>> > Error in (...) : 3 arguments passed to '(' which requires 1
>> >
>> > 20150123 21:48:01| Could not locate monocell CDF. Will create one for
>> > chip type...done
>> >
>> > 20150123 21:48:01|Retrieving monocell CDF...done
>> >
>> > ...
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