[BioC] Stuck with Yeast Tiling Array

[Joern Toedling]

Richard,

> Thanks Joern,
> The first part works great:
>
> > sampleNames(richard)
> [1] "./ucont.CEL" "./utest.CEL"

not sure, whether that preceding './' in front of every name is what you
would want, how about
sampleNames(richard) <- dir(pattern=".CEL", full.names=FALSE)
instead.
> I was worried that when i use the davidTiling dataset and i do
> sampleNames, each Cel file is preceeded by a number, so what i would
> expect to see is:
>
> [1] "./ucont.CEL"
> [2] "./utest.CEL"
this is just how a character vector displayed in your console, with the
ExpressionSet in davidTiling the single entries in that sampleNames
character vector are just too long such that only one can be displayed
per line. The number preceding each line simply indicates which element
of the vector this line starts with.
With your sampleNames the single entries are relatively short and all of
the can fit in one line, though.

>
> What I actually want to do is normalise the arrays, by using the
> normalize by reference function. I now get the following error:
>
>
> >isDNA = richard$nucleicAcid == "ucont"
> > isRNA = richard$nucleicAcid == "utest"
> > pm = PMindex(probeAnno)
> > bg= BGindex(probeAnno)
> > yn = normalizeByReference (richard [,isRNA] , reference = richard
> [,isDNA], pm = pm, background +     = bg)
>
> Error in normalizeByReference(richard[, isRNA], reference = richard[,  :
>         There is nothing to normalize in 'x'.

Have you checked the contents of isDNA and isRNA? And are "pm" and "bg"
reasonable and is "bg" a subset of "pm". Please refer to the vignettes
of davidTiling for more details on these. And does pData(richard) have a
column "nucleicAcid"? Since you only have two samples, it may be easier
to set
isDNA <- 1; isRNA <- 2
This is only useful, though, if the array with the cel file 'ucont.CEL'
really is a genomic-DNA-hybridization and "utest.CEL" an
RNA-hybridization. If not, the whole normalization by a genomic-DNA
hybridization may not be appropriate.

Best regards,
Joern