Hi Pierre:
I tried using
library(aroma.affymetrix)
cs <- AffymetrixCelSet$byName("KN01M013", chipType="HG-U133_Plus_2")
raw=extractMatrix(cs,verbose=verbose)
but the 'raw' only gives a list of all intensities. I want to have the
output looks like a probe - intensity pair. Do you know how to do it?
Thanks
Best,
On Aug 8, 5:48 pm, Pierre Neuvial <pie...@stat.berkeley.edu> wrote:
> Hi,
>
> The 'annotationData' directory should be directly in your working
> directory, as explained in the page "Setup: Location of annotation
> data files":http://aroma-project.org/node/66
>
> In your case, you need to change the current directory to ~/experiment/ by
>
> setwd("~/experiment/")
>
> (or by starting your R session from this directory). Then your command
>
> csR <- AffymetrixCelSet$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.
>
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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
traceback(), and 3) to post a complete code example.
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