Hi Cathrine. A few comments below.
On 30/07/2009, at 2:33 AM, Cathy Mitchell wrote: > To whom it may concern, > > Is there a way of median normalising across your arrays in > aroma.affymetrix or can you only quantile normalise? > Is there a way of finding out all the other methods that are > available in aroma.affymetrix as the only information I've been able > to find is through the google groups. There is a ScaleNormalization, but it appears to be specific to SNP chips. It should be quite easy to implement, if it is not there. Maybe Henrik can comment on that one. As for getting help, you can call: help.start() ... and then find the aroma.affymetrix package and a bunch of documents. > Is there a way to quantile normalise between replicate arrays only > instead of all of the arrays? > How does one pull out a single array from the cel set? Yes, you can do this with extract(). For example, say 'cs' is an AffymetrixCelSet object. You can extract the first 2 samples with: csSubset <- extract(cs, 1:2) Hope that helps. Mark > > Thank you very much. > > -- > Cathrine Mitchell > > > > > ------------------------------ Mark Robinson, PhD (Melb) Epigenetics Laboratory, Garvan Bioinformatics Division, WEHI e: m.robin...@garvan.org.au e: mrobin...@wehi.edu.au p: +61 (0)3 9345 2628 f: +61 (0)3 9347 0852 ------------------------------ --~--~---------~--~----~------------~-------~--~----~ 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. To post to this group, send email to aroma-affymetrix@googlegroups.com To unsubscribe from this group, send email to aroma-affymetrix-unsubscr...@googlegroups.com For more options, visit this group at http://groups.google.com/group/aroma-affymetrix?hl=en -~----------~----~----~----~------~----~------~--~---
