[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
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