tilingArray problems
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Last seen 10 weeks ago
EMBL European Molecular Biology Laborat…
07/11/2008 17:41 Anjan Purkayastha scripsit > 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 > Hi Anjan your plots (in attachments?) didn't go through. If you don't have your own http-server, you could post them e.g. at Flickr or Youtube. It would also be useful to provide the exact set of R expressions you used, and the output of sessionInfo(). Best wishes Wolfgang ------------------------------------------------------------------ Wolfgang Huber EBI/EMBL Cambridge UK http://www.ebi.ac.uk/huber
Normalization GO tilingArray Normalization GO tilingArray • 545 views

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