[Bioc-sig-seq] 3'-5' position of Affymetrix probe sets

[Steve Lianoglou]

Hi,

On Wed, Mar 2, 2011 at 11:49 AM, Christos Hatzis
<christos.hatzis at nuverabio.com> wrote:
> Hello,
>
> For many genes, as in the example below, there are more than one Affy probe
> sets that interrogate the same transcript.  Is there a way to rank those
> probe sets relative to their proximity to the 3' end of the gene?  I wasn't
> sure whether there are annotation packages that provide the genomic
> coordinates of the probes in a probe set.

In addition to other emails you got, you can also do this manually.

I believe you can get the probe sequences for u133plus2 chip (and others) here:

http://www.bioconductor.org/help/bioc-views/release/data/annotation/html/gahgu133plus2probe.html

You can realign those yourself either with tools in Biostrings, or
extract the sequences to an appropriate fasta file, realign with
something like bowtie (or whatever is your favorite aligner) and post
process the results with a mix of Rsamtools and a GenomicFeatures
database built from your annotations of choice.

-steve

>
>> testids <- c("206527_at","209459_s_at","209460_at")
>> library(biomaRt)
>> ensembl <- useMart("ensembl", dataset = "hsapiens_gene_ensembl")
> Checking attributes ... ok
> Checking filters ... ok
>> probAttrs <- c("affy_hg_u133a", "hgnc_symbol", "chromosome_name",
>        "start_position", "end_position", "strand")
>> testres <- getBM(attributes = probAttrs, filters = "affy_hg_u133a", values
> =
>        testids, mart = ensembl)
>> testres
>  affy_hg_u133a hgnc_symbol chromosome_name start_position end_position
> strand
> 1   209459_s_at        ABAT              16        8768422      8878432
> 1
> 2     209460_at        ABAT              16        8768422      8878432
> 1
> 3     206527_at        ABAT              16        8768422      8878432
> 1
>
> Thank you.
> -Christos
>
> Christos Hatzis, Ph.D.
> Nuvera Biosciences, Inc.
> 400 West Cummings Park, Suite 5350
> Woburn, MA 01801
>
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-- 
Steve Lianoglou
Graduate Student: Computational Systems Biology
 | Memorial Sloan-Kettering Cancer Center
 | Weill Medical College of Cornell University
Contact Info: http://cbio.mskcc.org/~lianos/contact