how to use R read CHP file
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zhu zhidong ▴ 40
@zhu-zhidong-1535
Last seen 7.1 years ago
Hi, I want to use R to extract data from affy .chp file I download affxparser package for R, but I can't get help form chelp files. can you give me an answer. zhidong zhu
affy affxparser affy affxparser • 2.5k views
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@kasper-daniel-hansen-2979
Last seen 3 months ago
United States
Hi Zhidong The standard way would actually be to use the "affy" package. In that package you will find the function ReadAffy which is a high-level function and read.affybatch which is a more low-level function with better control. Read the help pages, especially the eaxmple. You may read cdf files using the makecdfenv package, but if you are using a "standard" affy chip, you can download ready-to-use packages from Bioconductor (look at http://www.bioconductor.org/packages/data/ annotation/stable/src/contrib/html/ ) You could also use the affxparser package. You can use read.cel.complete which reads a single cel file (so you need to do it multiple times and glue it together) read.cel.intensities which extracts the intensities from multiple cel files but I would recommend that you stick to the affy package if you are a "new" user. Kasper On Dec 11, 2005, at 2:22 AM, zhu zhidong wrote: > > Hi, > > I want to use R to extract data from affy .chp file > I download affxparser package for R, but I can't get help form > chelp files. > can you give me an answer. > > zhidong zhu > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor
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Actually the CHP files are files containing pre-processed results eg MAS 5.0 or similar from MAS or GCOS. They are not the same as CDF files. As far as I know there is no current functionality for reading CHP files into BioConductor. Instead the recommended procedure is as Kasper recommends. Get hold of the CEL files for your data, if possible. Then read them using the routines in the affy package. Consider pre-processing your data using rma() or gcrma(). Hope that helps, Ben On Sun, 2005-12-11 at 09:31 -0800, Kasper Daniel Hansen wrote: > Hi Zhidong > > The standard way would actually be to use the "affy" package. In that > package you will find the function ReadAffy which is a high-level > function and read.affybatch which is a more low-level function with > better control. Read the help pages, especially the eaxmple. > > You may read cdf files using the makecdfenv package, but if you are > using a "standard" affy chip, you can download ready-to-use packages > from Bioconductor (look at http://www.bioconductor.org/packages/data/ > annotation/stable/src/contrib/html/ ) > > You could also use the affxparser package. You can use > read.cel.complete which reads a single cel file (so you need to do > it multiple times and glue it together) > read.cel.intensities which extracts the intensities from multiple > cel files > but I would recommend that you stick to the affy package if you are a > "new" user. > > Kasper > > > On Dec 11, 2005, at 2:22 AM, zhu zhidong wrote: > > > > > Hi, > > > > I want to use R to extract data from affy .chp file > > I download affxparser package for R, but I can't get help form > > chelp files. > > can you give me an answer. > > > > zhidong zhu > > -- Ben Bolstad <bmb at="" bmbolstad.com=""> http://bmbolstad.com
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I got a private email worded in such a way that I think Zhidong means cel/cdf files when (s)he talks about chp files. I could be wrong. Anyway, as Ben said, the chp files are not that interesting. Kasper On Dec 11, 2005, at 10:47 AM, Ben Bolstad wrote: > Actually the CHP files are files containing pre-processed results eg > MAS 5.0 or similar from MAS or GCOS. They are not the same as CDF > files. > As far as I know there is no current functionality for reading CHP > files > into BioConductor. > > Instead the recommended procedure is as Kasper recommends. Get hold of > the CEL files for your data, if possible. Then read them using the > routines in the affy package. Consider pre-processing your data using > rma() or gcrma(). > > Hope that helps, > > Ben > > > > > > On Sun, 2005-12-11 at 09:31 -0800, Kasper Daniel Hansen wrote: >> Hi Zhidong >> >> The standard way would actually be to use the "affy" package. In that >> package you will find the function ReadAffy which is a high-level >> function and read.affybatch which is a more low-level function with >> better control. Read the help pages, especially the eaxmple. >> >> You may read cdf files using the makecdfenv package, but if you are >> using a "standard" affy chip, you can download ready-to-use packages >> from Bioconductor (look at http://www.bioconductor.org/packages/data/ >> annotation/stable/src/contrib/html/ ) >> >> You could also use the affxparser package. You can use >> read.cel.complete which reads a single cel file (so you need to do >> it multiple times and glue it together) >> read.cel.intensities which extracts the intensities from multiple >> cel files >> but I would recommend that you stick to the affy package if you are a >> "new" user. >> >> Kasper >> >> >> On Dec 11, 2005, at 2:22 AM, zhu zhidong wrote: >> >>> >>> Hi, >>> >>> I want to use R to extract data from affy .chp file >>> I download affxparser package for R, but I can't get help form >>> chelp files. >>> can you give me an answer. >>> >>> zhidong zhu >>> > -- > Ben Bolstad <bmb at="" bmbolstad.com=""> > http://bmbolstad.com
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zhu zhidong ▴ 20
@zhu-zhidong-1537
Last seen 7.1 years ago
Hi, I want to use R to extract data from affy .chp file I download affxparser package for R, but I can't get help form chelp files. can you give me an answer. zhidong zhu
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