How about grabbing the intensities according to their index: raw=extractMatrix(cs,cells=df$cell,verbose=verbose)
Then you'll have them matched up to the 'df' data.frame. (Different numbers for your chip, of course) > dim(df) [1] 844550 16 > dim(raw) [1] 844550 33 Mark On Aug 10, 2011, at 12:31 AM, hsingjun cheung wrote: > Hi Mark: > > My idea is how we could know the intensity for each probe ? Using > these command: > library(aroma.affymetrix) > cs <- AffymetrixCelSet$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/ -- 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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