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?
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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