hi, a rookie question on tilingArray: what criteria does one use to set a value for nrStrata? all help will be appreciated. tia, anjan -- =========================================== anjan purkayastha, phd bioinformatics analyst whitehead institute for biomedical research nine cambridge center cambridge, ma 02142 purkayas [at] wi [dot] mit [dot] edu 703.740.6939

24/10/2008 21:32 Anjan Purkayastha scripsit > hi, > a rookie question on tilingArray: > what criteria does one use to set a value for nrStrata? > all help will be appreciated. > tia, > anjan > Hi Anjan I assume that you are refering to the parameter "nrStrata" of the function "normalizeByReference" in the "tilingArray" package. Good choices of the value are bounded: - above by the number of background features (if you have too few in a stratum, the estimation of the background correction becomes unprecise) and - below by the variability of the values in "refSig" within each stratum; the background correction assumes that probes within one stratum have the same (background signal) distribution. I found "nrStrata=10" a good choice for an Affymetrix array tiling a yeast gnome with 6.5 Mio probes - you will need to make your own exploratory analysis of these criteria for your array. -- Best wishes Wolfgang ------------------------------------------------------------------ Wolfgang Huber EBI/EMBL Cambridge UK http://www.ebi.ac.uk/huber