Perhaps something like this is what you want (note: different chip to what you are using)?
df <- readDataFrame(getCdf(cs), verbose=-80) [...snip...] head(df) unit unitName unitType unitDirection unitNbrOfAtoms group groupName 1 1 7892501 expression sense 4 1 7892501 2 1 7892501 expression sense 4 1 7892501 3 1 7892501 expression sense 4 1 7892501 4 1 7892501 expression sense 4 1 7892501 5 2 7892502 expression sense 4 1 7892502 6 2 7892502 expression sense 4 1 7892502 groupDirection groupNbrOfAtoms cell x y pbase tbase indexPos atom 1 sense 4 116371 870 110 C G 0 0 2 sense 4 943979 28 899 A T 1 1 3 sense 4 493089 638 469 T A 2 2 4 sense 4 907039 888 863 A T 3 3 5 sense 4 1033309 108 984 T A 0 0 6 sense 4 653512 411 622 T A 1 1 I'm not sure what object you have in mind when it comes to a probe- intensity pair, but this should give you all the info you might want (e.g. cell index, x/y physical location). HTH, Mark On Aug 9, 5:45 pm, Pierre Neuvial <pie...@stat.berkeley.edu> wrote: > 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/... > > 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 "aroma.affymetrix" group with > >> > websitehttp://www.aroma-project.org/. > >> > 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 websitehttp://www.aroma-project.org/. > > 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/
