thanks Benilton,

i have already done all this. everything works fine, i can read the cel
files, i installed and loaded the package, but my problem is, that i do not
know how to combine the intensity data from the CEL files with the
annotation in the bpmap package (created with the makePDpackage). there are
no probe ids that i can use to map between intensities and annotation, and
the ordering in the bpmap package is according to the genomic location, of
the cel files (i suppose) in the order of x and y coordinates on the chip.

so if i extract the values for the first ten probes in my "rawData" object
(exprs(rawData)[1:10, ] or pm(rawData)[1:10, ]), how can i get to the
genomic location of those?
by the way... i actually do not know how to extract the intensity values,
what's the difference between exprs and pm?

thanks, jo

On Feb 6, 2008 8:02 AM, Benilton Carvalho <bcarvalh@jhsph.edu> wrote:

> Hi,
>
> Once you use makePDpackage, you should install the created package and
> read the CEL files after that. The general algorithm is:
>
> 1) Build the (annotation) source package - using makePDpackage
> 2) Install the package created in (1)
> 3) read.celfiles()
> 3.1) if the CEL files headers point to a different reference, you'll
> need to use the "pkgname" argument of read.celfiles()
>
> For example:
>
> Step 1)
>
>  > makePDpackage("Sc03b_MF_v04.bpmap", "Sc03b_MF_v04.cif",
> type="tiling", manufacturer="affymetrix")
> affymetrix tiling
> The package will be called pd.sc03b.mf.v04
> Array identified as having 2560 rows and 2560 columns.
> Creating package in /data1/microarray/yeast/pd.sc03b.mf.v04
> [1] "pd.sc03b.mf.v04"
>
>
> That tells us that the (annotation) source package "pd.sc03b.mf.v04"
> was created. Now we have to install it.
>
> Step 2)
>
> On *NIX systems, you could quit R and type on your terminal:
>
> R CMD INSTALL /data1/microarray/yeast/pd.sc03b.mf.v04
>
> On Windows, the process is a little bit more complex:
>
> http://www.biostat.wisc.edu/~kbroman/Rintro/Rwinpack.html<http://www.biostat.wisc.edu/%7Ekbroman/Rintro/Rwinpack.html>
>
> Step 3) Back in R:
>
> library(oligo)
> celFiles <- list.celfiles(pathWhereCELfilesAre, full.names=TRUE)
> rawData <- read.celfiles(celFiles)
>
> Step 3.1) If it complains saying that the package is not installed,
> you should try:
>
> library(oligo)
> celFiles <- list.celfiles(pathWhereCELfilesAre, full.names=TRUE)
> rawData <- read.celfiles(celFiles, pkgname="pd.sc03b.mr.v04")
>
>
> best,
> b
>
>
> On Feb 6, 2008, at 1:43 AM, Johannes Rainer wrote:
>
> > hi,
> >
> > i am trying to analyze Affymetrix Promoter tiling arrays with R, but
> > have
> > not found a way to do this so far. first of all i want to import the
> > CEL
> > files, and to get the mapping between the probes and the genomic
> > locations.
> > reading the cel files is per se not so difficult, since the
> > affxparser and
> > oligo packages provide functions for that, but when it comes to
> > annotate the
> > probes i have difficulties. i generated a platformDesign object/
> > package with
> > the makePlatformDesign package (makePDPackage, version 1.2.0,
> > supplied the
> > bpmap file, and as parameter file1 the CIF file).
> > so far i got no problems, but now i do not know how to handle the
> > data i
> > read in (since there is also a lot of documentation missing for the
> > oligo
> > package).
> > how can i combine the information from the platformDesign object
> > with the
> > read CEL files? in the platformDesign there is the information of the
> > chromosomal location of the probes, but i suppose that the ordering
> > of the
> > probes in the platformDesign object differs from the read CEL files
> > (TilingFeatureSet class). i also checked all slots from the
> > platformDesign
> > object, but the slot "indexes" is an empty list. the environment
> > stored in
> > the "featureInfo" slot contains a "order_index", but there is no
> > description
> > about that, so i don not know if i should use this to reorder the
> > elelments
> > from the platformDesign, or the ordering of the elements in the
> > TilingFeatureSet.
> > can anyone please help here, or is there an other way to read
> > Affymetrix
> > tiling array data (and to combine the data with the probe annotation)?
> >
> > thanks in advance, jo
> >
> > --
> > Johannes Rainer, PhD
> > Tyrolean Cancer Research Institute
> > Innrain 66, 6020 Innsbruck, Austria
> > Tel.: +43 512 570485 33
> > Email: johannes.rainer@tcri.at
> >           johannes.rainer@i-med.ac.at
> >
> >       [[alternative HTML version deleted]]
> >
> > _______________________________________________
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> > Bioconductor@stat.math.ethz.ch
> > https://stat.ethz.ch/mailman/listinfo/bioconductor
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>
>


-- 
Johannes Rainer, PhD
Tyrolean Cancer Research Institute
Innrain 66, 6020 Innsbruck, Austria
Tel.: +43 512 570485 33
Email: johannes.rainer@tcri.at
           johannes.rainer@i-med.ac.at

	[[alternative HTML version deleted]]

