[BioC] Analysing expression with tiling arrays

Edwin Groot edwin.groot at biologie.uni-freiburg.de
Fri Sep 10 11:12:48 CEST 2010

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???


> 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

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