[BioC] R: Probe-level analysis of exon arrays using xps

[Lavorgna Giovanni]

Dear Cristian,
many thanks for your prompt answer. In my case, once I have the probe intensities, I would like to do the following two preliminary steps:
a) Remove probes that hybridize to multiple loci in the genome.
b) Remove probes that show a correlation coefficient below a certain threshold.
Then, I would like to calculate the differential expression in diseased vs. healthy samples for a few transcripts of mine by averaging the ratio of the probe intensities. I hope that the increased granularity and the reduced background of this method can give a better resolution to my analysis. As I said before, similar probe selection methods have been already described (see for example Xing Y, Kapur K, Wong WH. PLoS ONE. 2006 20;1:e88) and applied to genome wide studies.

In my case, after step a), I would like simply to dump the probes to a text file, select those of my interest and read them into to a spreadsheet in order to calculate the correlation coefficient and the fold-change of my transcripts. You already started to sketch the beginning of pipeline I should use: if I am not asking for too much, I would be grateful if you could elaborate it a little more to include also these final two steps.
Thanks again for your assistance and keep up the good work.
Giovanni

________________________________________
Da: cstrato [cstrato at aon.at]
Inviato: giovedì 18 agosto 2011 20.28
A: Lavorgna Giovanni
Cc: bioconductor at r-project.org
Oggetto: Re: [BioC] Probe-level analysis of exon arrays using xps

Dear Giovanni,

In principle you could do the background and normalization steps
separately, e.g.:
 > data.bg.rma <- bgcorrect.rma(data.exon, ...)
 > data.qu.rma <- normalize.quantiles(data.bg.rma, ...)

Now you have the normalized probes, however, you cannot do any
summarization such as median-polish or mean.

It is not quite clear to me how you want to proceed with the normalized
probe intensities?

Best regards
Christian
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On 8/18/11 7:08 PM, Lavorgna Giovanni wrote:
>
> As you guys know, there is a growing evidence showing that a probe-level analysis  (as opposed to a probeset-level or a gene-level analysis) could be useful in analyzing Exon arrays. I am currently analyzing several human exon chips (185!) on a 4 GB machine and I am using the xps package. I would like to stick to this software since it allows to manage several chips with the resources at hand and I was wondering if anyone has ever tried to perform probe level analysis using xps. Also, I would be grateful if anyone could point out alternative resources to perform this job.
> Thanks in advance.
> Giovanni
>
>
>
>
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Dai il tuo 5XMILLE al San Raffaele. Basta una firma.
Se firmi per la ricerca sanitaria del San Raffaele di Milano, firmi per tutti.
C.F. 03 06 42 80 153.
INFO: 5xmille at hsr.it - www.5xmille.org