Re: [aroma.affymetrix] Re: How to extract raw probe intensity from .CEL file
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 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
>> 11 7892501 expression sense 4 1
>> 7892501
>> 21 7892501 expression sense 4 1
>> 7892501
>> 31 7892501 expression sense 4 1
>> 7892501
>> 41 7892501 expression sense 4 1
>> 7892501
>> 52 7892502 expression sense 4 1
>> 7892502
>> 62 7892502 expression sense 4 1
>> 7892502
>> groupDirection groupNbrOfAtomscell x y pbase tbase indexPos
>> atom
>> 1 sense 4 116371 870 110 C G
>> 00
>> 2 sense 4 943979 28 899 A T
>> 11
>> 3 sense 4 493089 638 469 T A
>> 22
>> 4 sense 4 907039 888 863 A T
>> 33
>> 5 sense 4 1033309 108 984 T A
>> 00
>> 6 sense 4 653512 411 622 T A
>> 11
>>
>> 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 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
>>
>>> 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 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$byName("KN01M013",chipType="HG-U133_Plus_2")
>>
> should work.
>>
> Best,
>>
> Pierre
>>
> On Mon, Aug 8, 2011 at 5:29 PM, hsingjun cheung
>>
> wrote:
>> Hello:
>>
>> I searched the group but got no results ... So I want to know, how to
>> extract the raw probe intensity from .CEL file?
>>
>> The file structure on my computer is like:
>>
>> ~/experiemnt/
>> annotationData/
>> chipTypes/
>>HG-U133_Plus_2/
>> HG-U133_Plus_2.cdf
>> ~/experiment/
>> rawData/
>> KN01M013/
>> HG-U133_Plus_2/
>>KN01M013.CEL
>>
>> The .cdf file is downloaded
>> fromhttp://www.aroma-project.org/chipTypes/HG-U133_Plus_2
>>
>> When I run R under ~ directory:
>> library(aroma.affymetrix)
>> csR <- AffymetrixCelSet$byName("KN01M013",chipType="HG-U133_Plus_2")
>>
>> I got error msg:
>>
>> Error in list(`AffymetrixCelSet$byName("KN01M013", chipType = "HG-
>> U133_Plus_2")` = , :
>>
>> [2011-08-08 11:24:05] Exception: Could not locate a file for this chip
>> type: HG-U133_Plus_2
>> at throw(Exception(...))
>> at throw.default("Could not locate a file for this chip type: ",
>> paste(c(chipT
>> at throw("Could not locate a file for this chip type: ",
>> paste(c(chipType, tag
>> at method(sta
Re: [aroma.affymetrix] Re: How to extract raw probe intensity from .CEL file
Hi,
Have you tried using extractAffyBatch, which is documented here:
http://aroma-project.org/howtos/extractAffyBatch ?
As far as I understand you will need the Bioconductor annotation
package corresponding to your chip type to be installed, ie
source("http://www.bioconductor.org/biocLite.R";)
biocLite("hgu133plus2cdf")
This is discussed in this thread:
http://groups.google.com/group/aroma-affymetrix/browse_thread/thread/40e3950e52d73c1f/772e387a3163db56
Pierre
On Tue, Aug 9, 2011 at 4:34 AM, hsingjun cheung
wrote:
> Hi Pierre:
>
> Thanks. These functions work now. Do you know how to extract the raw
> intensity for each probe ?
>
> On Aug 8, 5:48 pm, Pierre Neuvial wrote:
>> Hi,
>>
>> The 'annotationData' directory should be directly in your working
>> directory, as explained in the page "Setup: Location of annotation
>> data files":http://aroma-project.org/node/66
>>
>> In your case, you need to change the current directory to ~/experiment/ by
>>
>> setwd("~/experiment/")
>>
>> (or by starting your R session from this directory). Then your command
>>
>> csR <- AffymetrixCelSet$byName("KN01M013",chipType="HG-U133_Plus_2")
>>
>> should work.
>>
>> Best,
>>
>> Pierre
>>
>> On Mon, Aug 8, 2011 at 5:29 PM, hsingjun cheung
>>
>>
>>
>>
>>
>>
>>
>> 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")` = , :
>>
>> > [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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>> > To post to this group, send email to aroma-affymetrix@googlegroups.com
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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.
>
>
> 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
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