Hi Jean-Paul, sorry, but MedianNormalization is still not implemented, but thanks to your reminder it got bumped up in the to-do list. I complete agree with your arguments - it's just a matter of finding time to implement it.
/Henrik On Sat, May 25, 2013 at 10:20 AM, Jean-Paul Abbuehl <jp.abbu...@gmail.com> wrote: > 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>: >> > >> > 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. > > -- -- 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.
