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 <zqznept...@gmail.com> 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
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>> >
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> --
> --
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> 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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