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

[Sean Davis]

Pia Sappl wrote:
> 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?
>   
I haven't used the package in a long time, but you might look at the 
tilingArray package.  Also, I would highly recommend reading some of the 
literature utilizing tiling arrays.  The analysis of such arrays is full 
of challenges and will probably require some customized analyses to 
answer specific biologic questions. 

Sean