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.
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/
