Re: [aroma.affymetrix] Questions on extracting probeset summaries
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$getVerbose(-8, timestamp = TRUE))
I'll investigate and fix this asap.
/Henrik
On Fri, Jan 23, 2015 at 7:37 AM, Henrik Bengtsson h...@biostat.ucsf.edu
wrote:
On Jan 23, 2015 7:36 AM, Henrik Bengtsson h...@biostat.ucsf.edu wrote:
This is odd for several reasons, e.g. I'm puzzled how you ended up with a
monocell CDF previously but now it gives an error. Let's troubleshoot
more...
What does troubleshoot() output directly after you get that error?
I meant traceback()
Henrik
On Jan 23, 2015 7:23 AM, Qingzhou Zhang zqznept...@gmail.com wrote:
Thanks, Henrik,
It seems that something went wrong with the monocell cdf file by
troubleshooting:
cdf
AffymetrixCdfFile:
Path: annotationData/chipTypes/HG-U133_Plus_2
Filename: HG-U133_Plus_2,monocell.CDF
File size: 4.88 MB (5116945 bytes)
Chip type: HG-U133_Plus_2,monocell
RAM: 0.46MB
File format: v4 (binary; XDA)
Dimension: 182x182
Number of cells: 33124
Number of units: 27604
Cells per unit: 1.20
Number of QC units: 9
So I have deleted the previous monocell cdf file in
annotationData/chipTypes/HG-U133_Plus_2 and re-create it by the following:
cdf - AffymetrixCdfFile$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 7.91757946 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 7.31757946 13.5 1424724 10.9
20150123 21:47:56| Number of cells per unit:
Min. 1st Qu. MedianMean 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
Re: [aroma.affymetrix] Questions on extracting probeset summaries
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 7.91757946 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 7.31757946 13.5 1424724 10.9 20150123 21:47:56| Number of cells per unit: Min. 1st Qu. MedianMean 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 8.61925843 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 7.85484388 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
Re: [aroma.affymetrix] Questions on extracting probeset summaries
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 7.91757946 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 7.31757946 13.5 1424724 10.9 20150123 21:47:56| Number of cells per unit: Min. 1st Qu. MedianMean 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 8.61925843 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 7.85484388 41.9 6516658 49.8 20150123 21:47:57|Writing...done 20150123 21:47:57| Creating CDF header
