[BioC] Analysing expression with tiling arrays

[January Weiner]

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.

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

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-------- Dr. January Weiner 3 --------------------------------------