Great. I've now made aroma.affymetrix 2.13.1 available, which is
installed the usual way:
source('http://callr.org/install#aroma.affymetrix";)
Anyone who reads this should update this way.
/Henrik
On Fri, Jan 23, 2015 at 2:57 PM, Qingzhou Zhang <zqznept...@gmail.com> wrote:
> Thanks!
>
> Seems working pretty well.
>
>> cdf <- AffymetrixCdfFile$byChipType("HG-U133_Plus_2")
>> cdfM <- getMonocellCdf(cdf, verbose=TRUE)
> Retrieving monocell CDF...
> Monocell chip type: HG-U133_Plus_2,monocell
> Locating monocell CDF...
> Pathname:
> Locating monocell CDF...done
> Could not locate monocell CDF. Will create one for chip type...
> Could not locate monocell CDF. Will create one for chip type...done
> Retrieving monocell CDF...done
>> print(cdfM)
> AffymetrixCdfFile:
> Path: annotationData/chipTypes/HG-U133_Plus_2
> Filename: HG-U133_Plus_2,monocell.CDF
> File size: 9.63 MB (10098009 bytes)
> Chip type: HG-U133_Plus_2,monocell
> RAM: 0.00MB
> File format: v4 (binary; XDA)
> Dimension: 246x245
> Number of cells: 60270
> Number of units: 54675
> Cells per unit: 1.10
> Number of QC units: 9
>
>
>
> On Saturday, 24 January 2015 03:52:43 UTC+8, Henrik Bengtsson wrote:
>>
>> Solved. Before finalize a release, would you mind making sure it
>> works on your end. Install aroma.affymetrix 2.13.0-9001 by running
>> the following in a fresh R session:
>>
>>
>> source('http://callr.org/install#HenrikBengtsson/aroma.affymetrix@2.13.0-9001')
>>
>> Then retry with
>>
>> library("aroma.affymetrix")
>> cdf <- AffymetrixCdfFile$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>
>> 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> 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" <zqzne...@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
>> >>> >
>> >>> > ...
>
> --
> --
> 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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--
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