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
>> > version of the package, 2) to report the output of sessionInfo() and
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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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version of the package, 2) to report the output of sessionInfo() and 
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