Hi, Ran tilingArray package on my dataset. But instead of the well- separated signal and noise intensities a la Huber et al I get a get a noisy data transformation (see normalizedbytilingArray). As a comparison I have plotted the Non-normalized signal intensities, Reference signal intensities and the Non-normalized intensity-divided-by-Reference intensity in the second plot (tilingArray_Normalization_1). It looks like the strong DNA hyb reference signal may be masking the differences in the signal intensities between transcribed and untranscribed regions. Anyone else having similar problems. Brief description of the array: it consists of non-overlapping 60mers tiled along the vaccinia virus genome sequence (ca 190kb)- there are about 6200 probes in all. We used 3micrograms of DNA for the reference array hybs and 1.2 micrograms of RNA for the expression hybs. Normalization was done with the weakest 5% of probes dropped. Thanks in advance. 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 ===========================================