Hi Andrew, Just thought I'd refer you to a discussion on the list a few weeks ago about removal of probesets, which might help. As I understand it, the problem is that you need to remove your probes (or probesets) from the cdf as well as your affybatch object, so that they match. There is a chunk of code written by Ariel Chernomoretz and modified by Jenny Drnevich which does exactly this. You can find it here: http://article.gmane.org/gmane.science.biology.informatics.conductor/9 869/match=remove+probes+cdf See also below for a thread to the discussion: http://search.gmane.org/?query=Amy+Mikhail+genefilter+questions&author =&group=gmane.science.biology.informatics.conductor&sort=relevance&DEF AULTOP=and&%5B=2&xP=amy%09mikhail%09genefilter%09questions&xFILTERS=Gs cience.biology.informatics.conductor---A It's quite versatile as you can apply the code and remove your probes either before anything or after background correction, for example (what stage is best would depend on what your set of removed probes does to the variance and standard errors, etc as Jim mentioned). Hope this helps, Amy ---------------------------------------------------------------------- ------- Thanks, Jim, for the thoughts below. Unfortunately, we are using a custom Affy chip design here, so those precomputed ones won't work for us. But we could certainly create a custom CDF file for our chip type too... ... but it surprises me somewhat that there isn't an alternate solution. First, what do people do with an AffyBatch object which was read in using the rm.mask option if it can't be used for further analyses? (Or is this a failing in how gcrma specifically deals with NAs?) And second, although custom CDFs would be great for dealing with ChipType-specific effects (e.g., SNPs), how do people deal with chip-specific effects (e.g., scratches and debris)? Just a couple of thoughts... Any additional ideas are welcome, but we'll be pushing ahead on custom CDFs in the mean time... Cheers, -andrew ------------------------------------------- Amy Mikhail Research student University of Aberdeen Zoology Building Tillydrone Avenue Aberdeen AB24 2TZ Scotland Email: a.mikhail at abdn.ac.uk Phone: 00-44-1224-272880 (lab) 00-44-1224-273256 (office)