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