[BioC] TilingArray Normalization

Anjan Purkayastha purkayas at wi.mit.edu
Fri Nov 28 17:50:55 CET 2008

I am trying to use the tilingArray normalization package for the 
following array:
total number of probes: 6490. (these are a set of non-overlapping, 
contiguous 60mer probes that span the vaccinia virus genome-~200kb)
total number of perfect matches: 6490.
total number of background probes: 1275.( the vaccinia genome is very 
densely packed so there are few untranscribed regions).
The above mentioned array is being use to assay the transcription of the 
viral genes over an infection time-course.

The probe intensities from DNA-hybs used for normalization are on 
average as strong as the non-normalized probe intensities from 
transcription assays.
 The "normalized" signal after the tilingArray normalization seem to be 
*noisier* than the non-normalized input.

I know there may not be enough material in this email for the Gurus to 
provide advice.
I'd be happy to provide more details- genomic map of normalized and 
non-normalized signal etc, but there seems to be a size limit to 
attachments for this forum.
Please let me know if you have any specific questions regarding the 
experiment and/or the data.

All advice/questions will be appreciated.

anjan purkayastha, phd
bioinformatics analyst
whitehead institute for biomedical research
nine cambridge center
cambridge, ma 02142

purkayas [at] wi [dot] mit [dot] edu  

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