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 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 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/
[aroma.affymetrix] Re: How to extract raw probe intensity from .CEL file
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 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
[aroma.affymetrix] Re: How to extract raw probe intensity from .CEL file
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
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 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 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 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$byName(KN01M013, chipType = HG-U133_Plus_2) Could anyone help me figure how this error happened ? And how to do it ( extract raw probe intensity ) in a right way ? Thanks -- When reporting problems on aroma.affymetrix, make sure 1) to
[aroma.affymetrix] Re: How to extract raw probe intensity from .CEL file
Hi Pierre: Thanks. These functions work now. Do you know how to extract the raw intensity for each probe ? On Aug 8, 5:48 pm, Pierre Neuvial pie...@stat.berkeley.edu wrote: Hi, The 'annotationData' directory should be directly in your working directory, as explained in the page Setup: Location of annotation data files:http://aroma-project.org/node/66 In your case, you need to change the current directory to ~/experiment/ by setwd(~/experiment/) (or by starting your R session from this directory). Then your command csR - AffymetrixCelSet$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 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/
[aroma.affymetrix] Re: How to extract raw probe intensity from .CEL file
Hi Pierre: I tried using library(aroma.affymetrix) cs - AffymetrixCelSet$byName(KN01M013, chipType=HG-U133_Plus_2) raw=extractMatrix(cs,verbose=verbose) but the 'raw' only gives a list of all intensities. I want to have the output looks like a probe - intensity pair. Do you know how to do it? Thanks Best, On Aug 8, 5:48 pm, Pierre Neuvial pie...@stat.berkeley.edu wrote: Hi, The 'annotationData' directory should be directly in your working directory, as explained in the page Setup: Location of annotation data files:http://aroma-project.org/node/66 In your case, you need to change the current directory to ~/experiment/ by setwd(~/experiment/) (or by starting your R session from this directory). Then your command csR - AffymetrixCelSet$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 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/
