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 I tried on other chiptypes, the same error was returned as well.
I have even cleared the ~/.Rcache/aroma.affymetrix/ folder, which could not
solve this problem at all.
On Friday, 23 January 2015 11:23:12 UTC+8, Henrik Bengtsson wrote:
>
> Thanks. I can *not* reproduce this, e.g.
>
> > ces
> ChipEffectSet:
> Name: GSE9890
> Tags: GRBC,QN,RMA,oligo
> Path: plmData/GSE9890,GRBC,QN,RMA,oligo/HG-U133_Plus_2
> Platform: Affymetrix
> Chip type: HG-U133_Plus_2,monocell
> Number of arrays: 10
> Names: GSM249671, GSM249672, GSM249673, ..., GSM249680 [10]
> Time period: 2015-01-17 09:43:28 -- 2015-01-17 09:43:35
> Total file size: 5.75MB
> RAM: 0.02MB
> Parameters: {}
>
> > ces[[1]]
> ChipEffectFile:
> Name: GSM249671
> Tags: chipEffects
> Full name: GSM249671,chipEffects
> Pathname:
> plmData/GSE9890,GRBC,QN,RMA,oligo/HG-U133_Plus_2/GSM249671,chipEffects.CEL
> File size: 589.25 kB (603394 bytes)
> RAM: 0.02 MB
> File format: v4 (binary; XDA)
> Platform: Affymetrix
> Chip type: HG-U133_Plus_2,monocell
> Timestamp: 2015-01-17 09:43:28
> Parameters: {probeModel: chr "pm"}
>
> > data <- extractDataFrame(ces, units=NULL, addNames=TRUE)
> > str(data)
> 'data.frame': 54675 obs. of 15 variables:
> $ unitName : chr "AFFX-BioB-5_at" "AFFX-BioB-M_at" "AFFX-BioB-3_at"
> "AFFX-BioC-5_at" ...
> $ groupName: chr "" "" "" "" ...
> $ unit : int 1 2 3 4 5 6 7 8 9 10 ...
> $ group : int 1 1 1 1 1 1 1 1 1 1 ...
> $ cell : int 1 2 3 4 5 6 7 8 9 10 ...
> $ GSM249671: num 1614 2691 2120 3904 2238 ...
> $ GSM249672: num 2612 4060 3301 5686 3280 ...
> $ GSM249673: num 2876 5178 4014 6861 4050 ...
> $ GSM249674: num 3328 5704 4350 7617 4505 ...
> $ GSM249675: num 3101 5455 4131 7735 4560 ...
> $ GSM249676: num 5081 8883 7173 10997 7188 ...
> $ GSM249677: num 2329 4186 3209 5853 3482 ...
> $ GSM249678: num 1723 3177 2353 5537 3141 ...
> $ GSM249679: num 1442 2458 2114 4285 2370 ...
> $ GSM249680: num 1469 2641 2154 4583 2582 ...
>
> So, let's start troubleshooting. First, you should see the exact same
> as I do for:
>
> > cdf <- getCdf(ces)
> > cdf
> 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: 3.34MB
> 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
>
> If not, that's where the problem is. If ok, then check this output:
>
> > map <- getUnitGroupCellMap(cdf)
> str(map)> str(map)
> Classes 'UnitGroupCellMap' and 'data.frame': 54675 obs. of 3
> variables:
> $ unit : int 1 2 3 4 5 6 7 8 9 10 ...
> $ group: int 1 1 1 1 1 1 1 1 1 1 ...
> $ cell : int 1 2 3 4 5 6 7 8 9 10 ...
>
> This "map" is essential in what information gets pulled out and
> returned. The number of rows/observations in this data frame should
> match the number of units in the 'cdf', i.e. 54,675 units.
>
> Let's start with that.
>
> Henrik
>
> On Thu, Jan 22, 2015 at 5:00 PM, Qingzhou Zhang <zqzne...@gmail.com
> <javascript:>> wrote:
> > Hi, Henrik,
> >
> > Thanks for the reply!
> >
> > Here is my code:
> >
> > library("aroma.affymetrix")
> > RawName = "Project1"
> > RawChipType = "HG-U133_Plus_2"
> >
> > ces <- doGCRMA(RawName, chipType = RawChipType)
> > data <- extractDataFrame(ces, units = NULL, addNames = TRUE)
> >
> > Here is the sessionInfo()
> >
> > R version 3.1.1 (2014-07-10)
> > Platform: x86_64-pc-linux-gnu (64-bit)
> >
> > locale:
> > [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
> > LC_TIME=en_GB.UTF-8
> > [4] LC_COLLATE=en_US.UTF-8 LC_MONETARY=en_GB.UTF-8
> > LC_MESSAGES=en_US.UTF-8
> > [7] LC_PAPER=en_GB.UTF-8 LC_NAME=C LC_ADDRESS=C
> > [10] LC_TELEPHONE=C LC_MEASUREMENT=en_GB.UTF-8
> > LC_IDENTIFICATION=C
> >
> > attached base packages:
> > [1] stats graphics grDevices utils datasets methods base
> >
> > other attached packages:
> > [1] aroma.light_2.2.1 aroma.affymetrix_2.13.0 aroma.core_2.13.0
> > R.devices_2.12.0
> > [5] R.filesets_2.6.0 R.utils_1.34.0 R.oo_1.18.2
> > affxparser_1.38.0
> > [9] R.methodsS3_1.6.2
> >
> > loaded via a namespace (and not attached):
> > [1] aroma.apd_0.5.0 base64enc_0.1-2 Cairo_1.5-7
> digest_0.6.8
> > DNAcopy_1.40.0
> > [6] matrixStats_0.13.0 PSCBS_0.43.0 R.cache_0.11.0
> R.huge_0.8.0
> > R.rsp_0.19.7
> > [11] tools_3.1.1
> >
> > Here is the traceback()
> >
> > 1: extractDataFrame(ces, units = NULL, addNames = TRUE)
> >
> >
> > I tried several times, but always got a data frame containing 27604 obj.
> :-(
> >
> > Thanks
> >
> >
> > On Friday, 23 January 2015 01:36:00 UTC+8, Henrik Bengtsson wrote:
> >>
> >> On Thu, Jan 22, 2015 at 5:44 AM, Qingzhou Zhang <zqzne...@gmail.com>
> >> wrote:
> >> > Hi Henrik,
> >> >
> >> > I was processing HG-U133_Plus_2 datasets. While extracting probeset
> >> > summaries(chip effects) as a data frame, I only got 27604 objs * n
> >> > variables.
> >> > I was hoping to get a data frame of 54675 objs., which equals the
> number
> >> > of
> >> > units in HG-U133_Plus_2 chip. Am I missing some steps, or processing
> the
> >> > wrong CEL files?
> >>
> >> Hard to say. Can you share your code (from beginning to end) showing
> >> what you're doing?
> >>
> >> Henrik
> >>
> >> >
> >> > Thanks a lot!
> >> >
> >> > --
> >> > --
> >> > 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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> 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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