[aroma.affymetrix] Re: Probe genomic location
The information the cdf file is giving me seems misleading: nbrOfCells(cdf) # 4,691,556 cellIndices - getCellIndices(cdf) #length(unlist(cellIndices)) # 4,358,832 The number of cells does not match the cell indices. ?? On May 18, 7:41 pm, Irene Pylypenko ipylype...@gmail.com wrote: chipType - Hs_PromPR_v02 cdf - AffymetrixCdfFile$byChipType(chipType, verbose=verbose) cs - AffymetrixCelSet$byName(GSE17125, cdf=cdf, verbose=verbose) acp - AromaCellPositionFile$byChipType(chipType) #dim 4359744 2 data - extractMatrix(cs) #dim: 4691556 66 On May 17, 5:29 pm, Henrik Bengtsson henrik.bengts...@aroma- project.org wrote: Hi, which chip type and CDF are you thinking of? Even better, please show the code how you got those numbers and we take it from there. /Henrik On Tue, May 17, 2011 at 1:53 PM, Irene Pylypenko ipylype...@gmail.com wrote: Hello, How do I find the genomic location of each probe (cell)? Specifically, a chromosome # and start site. Is this information stored in a AffymetrixCelSet object? I know the cdf object contains this information, via the AromaCellPositionFile file, but this gives me 4,359,744 probes, where as AffymetrixCelSet gives me 4,691,556. So I was wondering how I could map these two files. I know about the UGP files, but I believe it gives the unit locations, whereas I'm interested in probe location. Thanks, Irene -- 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: Probe genomic location
The information the cdf file is giving me seems misleading: nbrOfCells(cdf) # 4,691,556 cellIndices - getCellIndices(cdf) #length(unlist(cellIndices)) # 4,358,832 The number of cells does not match the cell indices. ?? On May 18, 7:41 pm, Irene Pylypenko ipylype...@gmail.com wrote: chipType - Hs_PromPR_v02 cdf - AffymetrixCdfFile$byChipType(chipType, verbose=verbose) cs - AffymetrixCelSet$byName(GSE17125, cdf=cdf, verbose=verbose) acp - AromaCellPositionFile$byChipType(chipType) #dim 4359744 2 data - extractMatrix(cs) #dim: 4691556 66 On May 17, 5:29 pm, Henrik Bengtsson henrik.bengts...@aroma- project.org wrote: Hi, which chip type and CDF are you thinking of? Even better, please show the code how you got those numbers and we take it from there. /Henrik On Tue, May 17, 2011 at 1:53 PM, Irene Pylypenko ipylype...@gmail.com wrote: Hello, How do I find the genomic location of each probe (cell)? Specifically, a chromosome # and start site. Is this information stored in a AffymetrixCelSet object? I know the cdf object contains this information, via the AromaCellPositionFile file, but this gives me 4,359,744 probes, where as AffymetrixCelSet gives me 4,691,556. So I was wondering how I could map these two files. I know about the UGP files, but I believe it gives the unit locations, whereas I'm interested in probe location. Thanks, Irene -- 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: Probe genomic location
chipType - Hs_PromPR_v02 cdf - AffymetrixCdfFile$byChipType(chipType, verbose=verbose) cs - AffymetrixCelSet$byName(GSE17125, cdf=cdf, verbose=verbose) acp - AromaCellPositionFile$byChipType(chipType) #dim 4359744 2 data - extractMatrix(cs) #dim: 4691556 66 On May 17, 5:29 pm, Henrik Bengtsson henrik.bengts...@aroma- project.org wrote: Hi, which chip type and CDF are you thinking of? Even better, please show the code how you got those numbers and we take it from there. /Henrik On Tue, May 17, 2011 at 1:53 PM, Irene Pylypenko ipylype...@gmail.com wrote: Hello, How do I find the genomic location of each probe (cell)? Specifically, a chromosome # and start site. Is this information stored in a AffymetrixCelSet object? I know the cdf object contains this information, via the AromaCellPositionFile file, but this gives me 4,359,744 probes, where as AffymetrixCelSet gives me 4,691,556. So I was wondering how I could map these two files. I know about the UGP files, but I believe it gives the unit locations, whereas I'm interested in probe location. Thanks, Irene -- When reporting problems on aroma.affymetrix, make sure 1) to run the latest version of the package, 2) to report the output of sessionInfo() and traceback(), and 3) to post a complete code example. You received this message because you are subscribed to the Google Groups aroma.affymetrix group with websitehttp://www.aroma-project.org/. To post to this group, send email to aroma-affymetrix@googlegroups.com To unsubscribe and other options, go tohttp://www.aroma-project.org/forum/ -- When reporting problems on aroma.affymetrix, make sure 1) to run the latest version of the package, 2) to report the output of sessionInfo() and traceback(), and 3) to post a complete code example. You received this message because you are subscribed to the Google Groups aroma.affymetrix group with website http://www.aroma-project.org/. To post to this group, send email to aroma-affymetrix@googlegroups.com To unsubscribe and other options, go to http://www.aroma-project.org/forum/
[aroma.affymetrix] Re: Probe genomic location
chipType - Hs_PromPR_v02 cdf - AffymetrixCdfFile$byChipType(chipType, verbose=verbose) cs - AffymetrixCelSet$byName(GSE17125, cdf=cdf, verbose=verbose) acp - AromaCellPositionFile$byChipType(chipType) #dim 4359744 2 data - extractMatrix(cs) #dim: 4691556 66 On May 17, 5:29 pm, Henrik Bengtsson henrik.bengts...@aroma- project.org wrote: Hi, which chip type and CDF are you thinking of? Even better, please show the code how you got those numbers and we take it from there. /Henrik On Tue, May 17, 2011 at 1:53 PM, Irene Pylypenko ipylype...@gmail.com wrote: Hello, How do I find the genomic location of each probe (cell)? Specifically, a chromosome # and start site. Is this information stored in a AffymetrixCelSet object? I know the cdf object contains this information, via the AromaCellPositionFile file, but this gives me 4,359,744 probes, where as AffymetrixCelSet gives me 4,691,556. So I was wondering how I could map these two files. I know about the UGP files, but I believe it gives the unit locations, whereas I'm interested in probe location. Thanks, Irene -- 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: Probe genomic location
chipType - Hs_PromPR_v02 cdf - AffymetrixCdfFile$byChipType(chipType, verbose=verbose) cs - AffymetrixCelSet$byName(GSE17125, cdf=cdf, verbose=verbose) acp - AromaCellPositionFile$byChipType(chipType) #dim 4359744 2 data - extractMatrix(cs) #dim: 4691556 66 On May 17, 5:29 pm, Henrik Bengtsson henrik.bengts...@aroma- project.org wrote: Hi, which chip type and CDF are you thinking of? Even better, please show the code how you got those numbers and we take it from there. /Henrik On Tue, May 17, 2011 at 1:53 PM, Irene Pylypenko ipylype...@gmail.com wrote: Hello, How do I find the genomic location of each probe (cell)? Specifically, a chromosome # and start site. Is this information stored in a AffymetrixCelSet object? I know the cdf object contains this information, via the AromaCellPositionFile file, but this gives me 4,359,744 probes, where as AffymetrixCelSet gives me 4,691,556. So I was wondering how I could map these two files. I know about the UGP files, but I believe it gives the unit locations, whereas I'm interested in probe location. Thanks, Irene -- 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/
