Hi Renaud see page 13 of the vignette for details on how to create a qcdef file http://bioconductor.org/packages/2.3/bioc/vignettes/simpleaffy/inst/do c/simpleAffy.pdf hth claire [[alternative HTML version deleted]]

Take a look at NetAffx/the probe control sequences file on the Affy website to find out what the probesets are for the control genes or look in the .psi file (I got the probesets below from here). alpha1 and alpha2 can stay as they are (as indicated in the .cif file), this should get you started claire array <insert cdf="" name="" here=""> alpha1 0.05 alpha2 0.065 spk bioB AFFX-r2-Ec-BioB-3_at spk bioC AFFX-r2-Ec-BioC-3_at spk bioD AFFX-r2-Ec-BioD-3_at spk creX AFFX-r2-P1-cre-3_at ratio actin3/actin5 AFFX-Sof-actin-3_a_at AFFX-Sof-actin-5_a_at ratio actin3/actinM AFFX-Sof-actin-3_a_at AFFX-Sof-actin-M_a_at ratio gapdh3/gapdh5 AFFX-Sof-gapdh-3_at AFFX-Sof-gapdh-5_at ratio gapdh3/gapdhM AFFX-Sof-gapdh-3_at AFFX-Sof-gapdh-M_at from the cif file ;P/A Call Parameters ;P/A: Thresholds MinAlpha1=0 MinAlpha2=0 Alpha1=0.050000 Alpha2=0.065000 DefAlpha1=0.050000 DefAlpha2=0.065000 MaxAlpha1=0.5 MaxAlpha2=0.5 2009/2/5 Renaud Gaujoux <renaud@cbio.uct.ac.za> Hi, > > I actually read the vignette but how do you get all the information needed > to create the file? I guess the qcdef file showed in vignette will not work > as it is for a sugar cane array (even changing the header name to > sugarcanecdf). > > Do I have to look by eye at the cdf file and extract the info? In that case > how do I know which control probe to chose? all of them? > It seems to me that the kind of information required can be found > automatically. I am not familiar with the Affy cdf format so I find it a bit > tricky to do that by hand. > Is there some procedure to follow to find the correct information in the > file? > > Thanks. > Renaud > > > claire wilson wrote: > >> Hi Renaud >> >> see page 13 of the vignette for details on how to create a qcdef file >> >> >> http://bioconductor.org/packages/2.3/bioc/vignettes/simpleaffy/inst /doc/simpleAffy.pdf >> >> hth >> >> claire >> > > -- http://claire.wilson.googlepages.com/ -- http://claire.wilson.googlepages.com/ [[alternative HTML version deleted]]

Hi, I actually read the vignette but how do you get all the information needed to create the file? I guess the qcdef file showed in vignette will not work as it is for a sugar cane array (even changing the header name to sugarcanecdf). Do I have to look by eye at the cdf file and extract the info? In that case how do I know which control probe to chose? all of them? It seems to me that the kind of information required can be found automatically. I am not familiar with the Affy cdf format so I find it a bit tricky to do that by hand. Is there some procedure to follow to find the correct information in the file? Thanks. Renaud claire wilson wrote: > Hi Renaud > > see page 13 of the vignette for details on how to create a qcdef file > > http://bioconductor.org/packages/2.3/bioc/vignettes/simpleaffy/inst/ doc/simpleAffy.pdf > > hth > > claire