[BioC] tilingArray problems

[Wolfgang Huber]

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