Hi all! >From gene expression analysis I know that non-specific filtering can be done for example with the nsFilter function by calculating the IQR and applying a cut off. Is it possible to do something similar with a 27k Illumina Bead array? Could I even use the nsFilter? Thanks Ninni -- output of sessionInfo(): -- -- Sent via the guest posting facility at bioconductor.org.

Hi, I would think so (at least I did it with 450 K data). Or just apply your method of choice for variance filtering (IQR or sd) to each probe and filter out your percentage of choice. Maybe plot a histogram of the variance measure to see it's distribution and see if there exists a logical cutoff. Kind regards, Martin -- M.A. (Martin) Rijlaarsdam MSc. MD Erasmus MC - University Medical Center Rotterdam Department of Pathology Room Be-432b Shipping adress: P.O. Box 2040, 3000 CA Rotterdam, The Netherlands Visiting adress: Dr. Molewaterplein 50, 3015 GE Rotterdam, The Netherlands Email: m.a.rijlaarsdam@gmail.com Mobile: +31 6 45408508 Telephone (work): +31 10 7033409 Fax +31 10 7044365 Website: http://www.martinrijlaarsdam.nl On Mon, Jun 16, 2014 at 3:15 PM, Ninni Nahm [guest] <guest@bioconductor.org> wrote: > Hi all! > > >From gene expression analysis I know that non-specific filtering can be > done for example with the nsFilter function by calculating the IQR and > applying a cut off. > > Is it possible to do something similar with a 27k Illumina Bead array? > Could I even use the nsFilter? > > Thanks > > Ninni > > > -- output of sessionInfo(): > > -- > > -- > Sent via the guest posting facility at bioconductor.org. > > _______________________________________________ > Bioconductor mailing list > Bioconductor@r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor > [[alternative HTML version deleted]]