Hi Mark: My idea is how we could know the intensity for each probe ? Using these command: library(aroma.affymetrix) cs <- AffymetrixCelSet$byName("KN01M013", chipType="HG-U133_Plus_2") raw=extractMatrix(cs,verbose=verbose)
I can see 'raw' is a list of intensities, but I don't know which probe ids they correspond to. Hope this clarifies. Thanks On Aug 9, 6:03 am, Mark Robinson <markrobinson....@gmail.com> wrote: > 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/