Thanks!
Seems working pretty well.
> cdf <- AffymetrixCdfFile$byChipType("HG-U133_Plus_2") > cdfM <-
> getMonocellCdf(cdf, verbose=TRUE) Retrieving monocell CDF... Monocell chip
> type: HG-U133_Plus_2,monocell Locating monocell CDF... Pathname: Locating
> monocell CDF...done Could not locate monocell CDF. Will create one for chip
> type... Could not locate monocell CDF. Will create one for chip
> type...doneRetrieving monocell CDF...done> print(cdfM)AffymetrixCdfFile:
Path: annotationData/chipTypes/HG-U133_Plus_2
Filename: HG-U133_Plus_2,monocell.CDF
File size: 9.63 MB (10098009 bytes)
Chip type: HG-U133_Plus_2,monocell
RAM: 0.00MB
File format: v4 (binary; XDA)
Dimension: 246x245
Number of cells: 60270
Number of units: 54675
Cells per unit: 1.10
Number of QC units: 9
On Saturday, 24 January 2015 03:52:43 UTC+8, Henrik Bengtsson wrote:
>
> Solved. Before finalize a release, would you mind making sure it
> works on your end. Install aroma.affymetrix 2.13.0-9001 by running
> the following in a fresh R session:
>
> source('
> http://callr.org/install#HenrikBengtsson/aroma.affymetrix@2.13.0-9001')
>
> Then retry with
>
> library("aroma.affymetrix")
> cdf <- AffymetrixCdfFile$byChipType("HG-U133_Plus_2")
> cdfM <- getMonocellCdf(cdf, verbose=TRUE)
> print(cdfM)
>
> If it complains about a pre-existing *.tmp file, remove that one an retry.
>
> As soon as you confirm it works, I'll make aroma.affymetrix 2.13.1
> available, because this was a critical bug(*).
>
> Thanks for the report
>
> /Henrik
>
> (*) DETAILS: Turns out to be due to a single stray newline. It should have
> been
>
> affxparser::writeCdfUnits(...)
>
> but it was:
>
> affxparser::writeCdfUnits
> (...)
>
> Despite running 24 hours of regular package testing, this piece of
> code was never tested. I've now added an explicit test on creating
> and re-creating monocell CDF.
>
> On Fri, Jan 23, 2015 at 8:49 AM, Henrik Bengtsson <h...@biostat.ucsf.edu
> <javascript:>> wrote:
> > 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
> <javascript:>> wrote:
> >>
> >> On Jan 23, 2015 7:36 AM, "Henrik Bengtsson" <h...@biostat.ucsf.edu
> <javascript:>> 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" <zqzne...@gmail.com
> <javascript:>> 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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