I am trying to process Affymetrix array data from the new rat chip (RAT230_2). We followed the vignette on setting up the new rat230-2.cdf file and all seemed fine (readaffy, rnadeg..., rma, etc.) until I tried (simpleaffy) qc.stats ERROR: I am sorry I donot know spike probes on rat230.2.cdf Do I need the new simpleaffy (last download Mar 2004), do I need the new R (currently running 1.8.1, on Linux)? or is there an additional script I need to run to inform R of the new parameters (spikes, etc.) for the RAT230_2? Your help is appreciated. Kim M. Gernert --- [[alternative HTML version deleted]]

Hi Kim, The new version of simpleaffy has a lot of bug fixes and stuff in it, so I'd suggest using it anyway... ;-) The qc.stats code needs to know which chip you're using, to pick the right spike probes - and detection p-value stuff needs to use it to work out which alpha1 and alpha2 parameters to use... I'm going to modify the code so you can specify the probes you wish to use and stuff like that. In the next day or two I'll add the rat2302cdf to the lists and upload a new version... Cheers, Crispin -----Original Message----- From: bioconductor-bounces@stat.math.ethz.ch [mailto:bioconductor-bounces@stat.math.ethz.ch] On Behalf Of Kim Gernert Sent: 23 April 2004 20:35 To: bioconductor@stat.math.ethz.ch Subject: [BioC] Affy Bioconductor with Rat230_2 chips I am trying to process Affymetrix array data from the new rat chip (RAT230_2). We followed the vignette on setting up the new rat230-2.cdf file and all seemed fine (readaffy, rnadeg..., rma, etc.) until I tried (simpleaffy) qc.stats ERROR: I am sorry I donot know spike probes on rat230.2.cdf Do I need the new simpleaffy (last download Mar 2004), do I need the new R (currently running 1.8.1, on Linux)? or is there an additional script I need to run to inform R of the new parameters (spikes, etc.) for the RAT230_2? Your help is appreciated. Kim M. Gernert --- [[alternative HTML version deleted]] _______________________________________________ Bioconductor mailing list Bioconductor@stat.math.ethz.ch https://www.stat.math.ethz.ch/mailman/listinfo/bioconductor -------------------------------------------------------- This email is confidential and intended solely for the use o...{{dropped}}