HI Henrik, I would like to do MedianNormalization with the newest aroma.affymetrix package. Have you been able to fix it since 2009? I still could not find any answer in the documentation. Median normalization is recommended for co-expression analysis analysis because QuantileNormalization could affect the relationship between pairs of coexpressed genes.
If not, could you suggest me another package I could use? Is limma my only option ? Looking forward hearing from you Best Jean-paul. Le jeudi 13 août 2009 18:42:34 UTC+2, Henrik Bengtsson a écrit : > > Hi, > > sorry, but the ScaleNormalization class is not working correctly and > should not be used. I'm not sure when I'll be able to fix it. Thus, > there is no way to do plain median scale normalization. > > In case anyone wants to dig into this, this class is actually supposed > to be replaced by the ScaleNormalization3 class and that's the one > that is not ready/working well. > > /Henrik > > 2009/8/10 CathyMitchell <cathrine...@gmail.com <javascript:>>: > > > > Hi Mark, > > > > Thank you very much. > > This does help. > > Although I'm not really sure what the ScaleNormalize does? > > > > On Jul 31, 1:31 pm, Mark Robinson <mrobin...@wehi.edu.au> wrote: > >> 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 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/ --- You received this message because you are subscribed to the Google Groups "aroma.affymetrix" group. To unsubscribe from this group and stop receiving emails from it, send an email to aroma-affymetrix+unsubscr...@googlegroups.com. For more options, visit https://groups.google.com/groups/opt_out.
