Hi,
Have you tried using extractAffyBatch, which is documented here:
http://aroma-project.org/howtos/extractAffyBatch ?
As far as I understand you will need the Bioconductor annotation
package corresponding to your chip type to be installed, ie
source("http://www.bioconductor.org/biocLite.R";)
biocLite("hgu133plus2cdf")
This is discussed in this thread:
http://groups.google.com/group/aroma-affymetrix/browse_thread/thread/40e3950e52d73c1f/772e387a3163db56
Pierre
On Tue, Aug 9, 2011 at 4:34 AM, hsingjun cheung
<hsingjun.ch...@gmail.com> wrote:
> Hi Pierre:
>
> Thanks. These functions work now. Do you know how to extract the raw
> intensity for each probe ?
>
> On Aug 8, 5:48 pm, Pierre Neuvial <pie...@stat.berkeley.edu> wrote:
>> Hi,
>>
>> The 'annotationData' directory should be directly in your working
>> directory, as explained in the page "Setup: Location of annotation
>> data files":http://aroma-project.org/node/66
>>
>> In your case, you need to change the current directory to ~/experiment/ by
>>
>> setwd("~/experiment/")
>>
>> (or by starting your R session from this directory). Then your command
>>
>> csR <- AffymetrixCelSet$byName("KN01M013",chipType="HG-U133_Plus_2")
>>
>> should work.
>>
>> Best,
>>
>> Pierre
>>
>> On Mon, Aug 8, 2011 at 5:29 PM, hsingjun cheung
>>
>>
>>
>>
>>
>>
>>
>> <hsingjun.ch...@gmail.com> wrote:
>> > Hello:
>>
>> > I searched the group but got no results ... So I want to know, how to
>> > extract the raw probe intensity from .CEL file?
>>
>> > The file structure on my computer is like:
>>
>> > ~/experiemnt/
>> > annotationData/
>> > chipTypes/
>> > HG-U133_Plus_2/
>> > HG-U133_Plus_2.cdf
>> > ~/experiment/
>> > rawData/
>> > KN01M013/
>> > HG-U133_Plus_2/
>> > KN01M013.CEL
>>
>> > The .cdf file is downloaded
>> > fromhttp://www.aroma-project.org/chipTypes/HG-U133_Plus_2
>>
>> > When I run R under ~ directory:
>> > library(aroma.affymetrix)
>> > csR <- AffymetrixCelSet$byName("KN01M013",chipType="HG-U133_Plus_2")
>>
>> > I got error msg:
>>
>> > Error in list(`AffymetrixCelSet$byName("KN01M013", chipType = "HG-
>> > U133_Plus_2")` = <environment>, :
>>
>> > [2011-08-08 11:24:05] Exception: Could not locate a file for this chip
>> > type: HG-U133_Plus_2
>> > at throw(Exception(...))
>> > at throw.default("Could not locate a file for this chip type: ",
>> > paste(c(chipT
>> > at throw("Could not locate a file for this chip type: ",
>> > paste(c(chipType, tag
>> > at method(static, ...)
>> > at AffymetrixCdfFile$byChipType(chipType)
>> > at method(static, ...)
>> > at AffymetrixCelSet$byName("KN01M013", chipType = "HG-U133_Plus_2")
>>
>> > Could anyone help me figure how this error happened ? And how to do
>> > it ( extract raw probe intensity ) in a right way ? Thanks
>>
>> > --
>> > 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.
>>
>> > You received this message because you are subscribed to the Google Groups
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>> > To post to this group, send email to aroma-affymetrix@googlegroups.com
>> > To unsubscribe and other options, go tohttp://www.aroma-project.org/forum/
>
> --
> 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.
>
>
> You received this message because you are subscribed to the Google Groups
> "aroma.affymetrix" group with website http://www.aroma-project.org/.
> To post to this group, send email to aroma-affymetrix@googlegroups.com
> To unsubscribe and other options, go to http://www.aroma-project.org/forum/
>
--
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.
You received this message because you are subscribed to the Google Groups
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