Hi, Sorry for the indistinctness. You are correct; these are indeed R-packages (CDF environments), thus not *files*. However, it won't be much effort to also make them available as files. I/we will have a look at it the next couple of days. We will also check the links/info and update them when needed. Guido
-----Original Message----- From: aroma-affymetrix@googlegroups.com [mailto:aroma-affymetrix@googlegroups.com] On Behalf Of Henrik Bengtsson Sent: Friday, December 07, 2012 17:51 To: aroma-affymetrix@googlegroups.com Subject: Re: [aroma.affymetrix] Gene 2.0 ST arrays Hi. On Fri, Dec 7, 2012 at 5:21 AM, Hooiveld, Guido <guido.hooiv...@wur.nl> wrote: > Hi, > To follow up on Henrik's suggestion: we recently have made > Bioconductor-compatible ('unofficial') CDFs for the STv2.0/2.1 arrays as > well, essentially using the PD.Info packages. Please find them here: > http://nmg-r.bioinformatics.nl/ This great. To clarify, are you creating/releasing CDF *files*, or only the various flavors of R packages containing that information? I see that you are referring to 'PdInfo2Cdf.R'(*) on the site, which indicates CDF files, but I cannot find such. (*) BTW, that script has now been replaced by http://aroma-project.org/howtos/createCdfFromBioconductorPlatformDesignInfo Thanks, Henrik > HTH, > Guido > > -----Original Message----- > From: aroma-affymetrix@googlegroups.com > [mailto:aroma-affymetrix@googlegroups.com] On Behalf Of Henrik > Bengtsson > Sent: Thursday, December 06, 2012 21:45 > To: aroma-affymetrix@googlegroups.com > Subject: Re: [aroma.affymetrix] Gene 2.0 ST arrays > > On Thu, Dec 6, 2012 at 5:54 AM, Maria Traka <maria.tr...@ifr.ac.uk> wrote: >> Hi guys, >> probably you've already given the answer somewhere but can i use >> aroma.affymetrix to analyse Affymetrix 2.0 ST arrays (human and mouse)? >> Presumably the same way as 1.0 arrays? > > I'm not working with those myself, and I don't know the exact design details > on those chips, but, yes, most likely the same way as the previous ST arrays. > > What is not available out of the box is a CDF file for these 2.0 ST > arrays (i.e. HuGene-2_0-st-v1 and ). Unless you find such CDFs from > the various groups providing custom CDFs, you need to create them > yourselves. Here you've got a few options, but I would try with > what's explained in how-to page 'Create a CDF file from Bioconductor > Platform Design (PD) Info package', which you find via > http://aroma-project.org/howtos/ > > /Henrik > >> >> Thanks in advance, >> Maria >> >> -- >> 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/ > > > > > -- > 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/ -- 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/
