[BioC] applicability of tilingArray package

[Wolfgang Huber]

Hi Michael,

there are two separate issues:
(i) finding the transcribed regions, separately in each of the samples
(wt, mut).
(ii) finding the differentially transcribed regions.

For (i), you could use an approach similar to that in the David et al.
and Huber et al. papers. Since you don't have the DNA reference hybes,
you could use the MM probes. This is described in Section 4.2 of the
vignette
http://www.bioconductor.org/packages/2.3/bioc/vignettes/tilingArray/inst/doc/assessNorm.pdf
and as the benchmarks in Section 5 show, it is not quite as good, but
still pretty good.

Don't think of this in terms of "normalising" the mutant against the
"wt" type, that doesn't make much sense.

For (ii), if you want to segment e.g. a probe-wise (moderated)
t-statistic, the piecewise constant model using in the tilingArray
package is not useful. A running window approach (like in TAS) makes
sense, the hard part is of course tuning its parameters.

AfaIk, there are methods for (i) and (ii) separately, and to join /
align them, the approaches are ad hoc. It would be nice if there were a
clean method that does (i) and (ii) jointly - maybe someone else has
insights in this?

Best wishes
 Wolfgang

------------------------------------------------------------------
Wolfgang Huber  EBI/EMBL  Cambridge UK  http://www.ebi.ac.uk/huber


04/11/2008 16:42 Michael Palumbo scripsit
> hello,
> 
> i have general questions regarding the applicability of the tilingArray
> package to my problem/data. i've used bioconductor in the past, but by
> no means am i an expert.
> 
> i have data from affy yeast tiling arrays - 3 mut and 3 wild type. i've
> run affy's TAS program on the CEL files - as a two sample analysis, ie,
> comparing wt to mut and viewed the results in IGB. my initial goal is to
> segment the results as was done in David et al, PNAS 2006. it seems to
> me there are fundamental differences in my data and the data of David et
> al. e.g., the normalization step described in tilingArray doc uses DNA
> hybridized to the chips as a reference - i don't have that, although i
> do have the wt data. a colleague thought i might be able to use the wt
> data in the normalization step, but that doesn't seem quite right to me.
> it is also described that normalization can occur by MM probes - maybe i
> can normalize the mut chip data w/ MM probes and completely ignore the
> wt data? i realize that if i did that, the result would no longer be a
> comparison of mut and wt and what i would 'see' would be different from
> what i currently see in IGB of the two sample TAS analysis. this also
> seems like it's not the best approach.
> 
> on the other hand, again, all i really want to do is segment the
> two-sample analysis that i've done. is there anything wrong with using
> the results of TAS's analysis? TAS does a normalization and has
> bandwidth averaging - as a non-expert, these are convenient and seem
> good to me.
> 
> thanks in advance for any and all responses/thoughts,
> mike palumbo
>