[BioC] Analysing expression with tiling arrays

[Edwin Groot]

On Fri, 10 Sep 2010 09:30:11 +0200
 January Weiner <january.weiner at mpiib-berlin.mpg.de> wrote:
> Dear all,
> 
> I have two tiling arrays of a bacterial genome. Unfortunately, I do
> not have the original files (like the bpmap / cel files for Affy
> tiling chips), just lists of spot intensities in two conditions for
> each probe (i.e. two values for each probe), and a list of gene
> positions on the genome. Several probes map on a each gene. The
> genome
> is not publicly available yet.
> 

Hello January,
If the tiling array is from Affymetrix, the bpmap files exist. To start
with you should track them down because they give the necessary
annotation and position information.
I am assuming you want to measure RNA translation using this tiling
array platform. That should be a fairly trivial analysis once you get
the data into an Expression Set object.
Is the data from GEO???

Edwin

> What would be the best way to tackle this? I thought that I might
> just
> calculate the logFC for each probe, and then, for each gene, run a
> one
> sample t-test of the corresponding probe logFC values; then correct
> for multiple testing.
> 
> Would that make sense? I looked up the approach described in Toedling
> and Huber in 2008 PLoC Comp Biol (doi:10.1371/journal.pcbi.1000227)
> but this is not exactly what I had in mind; rather than looking for
> enriched regions, I'm more interested in focusing on the genes
> directly -- as a bacterial genome is densely packed with probes and
> genes (I have 10-30 probes per gene).
> 
> Best regards,
> 
> January
> 
> --
> -------- Dr. January Weiner 3 --------------------------------------
> 
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Dr. Edwin Groot, postdoctoral associate
AG Laux
Institut fuer Biologie III
Schaenzlestr. 1
79104 Freiburg, Deutschland
+49 761-2032945