[BioC] tilingArray problems
purkayas at wi.mit.edu
Fri Nov 7 18:41:50 CET 2008
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 purkayastha, phd
whitehead institute for biomedical research
nine cambridge center
cambridge, ma 02142
purkayas [at] wi [dot] mit [dot] edu
More information about the Bioconductor