[BioC] Stuck with Yeast Tiling Array

[Joern Toedling]

Hello Richard,

the column nucleicAcid is part of the AnnotatedDateFrame object that
describes the samples in the ExpressionSet. There are different ways to
create such, have a look at the help pages for that class and the
'ExpressionSet'. It is assigned using the phenoData method then.

Richard Harrison wrote:
> I'm starting to understand now. I am a total beginner at R, so all
> this is very new. How do i make an equivalent of the
> davidTiling$nucleicAcid ? If I type that i see this:
>
> > davidTiling$nucleicAcid
> [1] genomic DNA genomic DNA genomic DNA poly(A) RNA poly(A) RNA
> poly(A) RNA
> [7] total RNA   total RNA
> Levels: genomic DNA poly(A) RNA total RNA
>
> I need to create a similar thing for my (richard) data set. Any ideas?
> my isDNA and isRNA, are both empty at the moment...which is why it
> isn't working!
>
> I have two DNA samples (and i'm just treating one as RNA) so I can
> work through the programs and see how it all works and where I need to
> get things modified, before I do a large batch of arrays (I've been
> messing with salt conditions so I need to see that these arrays
> actually have stuff hybed!!)
>
> All I actually want to do is an equivalent to rma, but i think that
> the tilingArray/davidTiling libraries are the only resources available
> at the moment.. i think!?

I am not sure whether you would want to use the function
normalizeByReference at all. In our case, we had poly-A-RNA samples and
direct genomic hybridization and we discovered that using the genomic
DNA for normalization of the RNA samples worked much better than other
probe-based background corrections and normalizations for improving the
signal-to-noise ratio. That's what the function is for.
There definitely are lots of other functions in other Bioconductor
packages that you can use for quality assessment of your arrays and for
background correction of your intensity data. The packages "affy" and
"oligo" may be good places to start.
I would suggest yougive a description of your samples and arrays and
what you want to analyze with these arrays to the list and I am sure
people who have have done similar analyses will be happy to give some
suggestions on other packages.
Sorry that I cannot be of more help at the moment.

Regards,
Joern