[BioC] Identification of unannotated transcripts using Arabidopsis 1.0R Tiling Arrays

Pia Sappl pia.sappl at sci.monash.edu.au
Mon Jul 9 08:29:44 CEST 2007


Dear Tiling Array Users

We have recently performed an Arabidopsis Tiling Array experiment to 
assess differential expression between mock treated and dex treated 
samples at 4 and 12 h after dex treatment (2 biological paired 
replicates = 8 chips in total).  ie mock 4h versus dex 4 h and mock 12 h 
vs dex 12 h.  As part of our analysis we would like to identify regions 
of DNA that do not fall within annotated exons (ie unannotated genes).  
Is anyone aware of an existing R algorithm we could use (or perhaps with 
minimal modifications) that would do this?  So far we have used TAS 
(Affymetrix software) to normalise the data and define regions of 
positive expression.  We have also used IGB (Affymetrix genome browser) 
to manually inspect the results.  However, we would like to take a more 
automated and objective approach using R.  Finally, has anyone used the 
Tiling Array to identify differential expression? And if so, what 
approach was used?

Thankyou
Pia


-----------------------
Dr Pia Sappl
Monash University



More information about the Bioconductor mailing list