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
> <javascript:>> 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!
> >
> > --
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--
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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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