Hi.
On Wed, Jun 6, 2012 at 9:23 AM, Hyuna Yang <[email protected]> wrote:
>
> Hi all,
>
> I have custom array (similar to human Exon array) and try to study
> alternative splicing using FIRMA.
> i) in theory, I think I can use FIRMA, but wonder that's possible at current
> aroma.affymetrix setup.
Yes, given that your chip has probes for the exons, that should work.
AFAIK, there is nothing in FIRMA that is hard-wired to the human exon
arrays per se.
> ii) if that's possible, what should be a chipType (i.e. can I use any human
> exon array such as chipType <- "HuEx-1_0-st-v2" )
You should use the formal chip type label as given by Affymetrix.
Presumably you already have CEL files, correct? If so, you can get
the chip type from the CEL file header, i.e.
library("affxparser");
hdr <- readCelHeader("MyCelFile.CEL");
str(hdr);
chipType <- hdr$chiptype;
print(chipType);
That's the chip type you should use, e.g.
rawData/MyDataSet/<chipType>/*.CEL and
annotationData/chipTypes/<chipType>/<chipType>,<tags>.CDF.
> iii) is there anything else I need to consider in terms of algorithm
> implementation since this is a custom array?
The major task is for you to setup a "custom" CDF file for this chip
type that defines the transcripts and their exons. This *will*
require that you know R and understand how the Affymetrix CDF
structure works. Have a look at
http://aroma-project.org/chipTypes/HuEx-1_0-st-v2
and you'll see that there are different ways to do this and different
sources to use, e.g. Ensemble and RefSeq. There is probably also some
information on http://aroma-project.org/howtos/ related to this that
the FIRMA authors scribbled down.
Hope this helps
/Henrik
>
> Thank you so much!
> Hannah
>
> --
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>
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--
When reporting problems on aroma.affymetrix, make sure 1) to run the latest
version of the package, 2) to report the output of sessionInfo() and
traceback(), and 3) to post a complete code example.
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