[BioC] PLANdbAffy + Alternative Exon Annotation +XPS, aroma, oligo, RMAExpress

[Benilton Carvalho]

oligo uses further annotation information contained in the files you
mention, and so does xps.

regarding memory use, you can just load the 'ff' package and oligo
will automatically use that to reduce memory footprint.

best,

b

On 7 December 2010 14:09,  <B.Misovic at lumc.nl> wrote:
> Dear Roman, all
>
>
>
>  Recently we tried your version of Annotation files for Gene 1.0 ST
> array that your team built from PLANdbAffy DB . I encountered some
> problems so I hope you can help.
>
>
>
> You provide nice CDF and Affy PGF/CLF files , but, the PGF/CLF were not
> useful in  bioConductor packages for affy Exon/Gene type arrays ,namely:
> oligo  & XPS as they require annotation file in csv format. I tried the
> annotation csv file from Affymetrix and after that from PLANdbAffy DB.
> The PLANdbAffy  csv file is very different from Affymetrix one so import
> is not possible (actually csv file on the website is TAB delimited
> instead of comma so problem already starts there , and  it requires
> reformatting).
>
>
>
> Christian from XPS was kind to inform me that :
>
>
>>... PLANdbAffy annotation  columns have nothing to do with the
> Affymetrix
>>annotation columns. Thus xps will not read these annotation files.
>
>>Alternative annotation files must contain exactly the same columns as
>
>>the Affymetrix annotation files.
>
>
>
>>For whole genome and exon arrays it is not possible to use only the
> PGF->files w/o the annotation files, since I extract most of the
> important >information from the probeset-annotation file first, so this
> file is >absolutely essential. For example, column "level" contains the
> information >Core/Extended/Full, see the corresponding annotation README
> files for an >explanation of all columns.
>
>
>
>>xps  error you get simply says that their PGF-file does not contain the
>>AFFX controls, so maybe adding the AFFX controls to their PGF-file
> might >help. However, as you mention, they use their own Probesetids,
> which will >not match the Probesetids of the Affymetrix annotation
> files, thus it may >not work anyhow.
>
>
>
>>It is not quite clear to me why they created their own PGF-file. The
>>Affymetrix PGF-file contains only 1-4 probes for each probeset, where
> each >exon consists of one or more probesets, thus the probability that
> a probe >within a probeset is not correct should be pretty small.
> However, a >probeset could be mapped to a wrong exon/gene or no gene at
> all, so it >should be sufficient to correct the Affymetrix annotation
> files.
>
>
>
>   The tools like RMAExpress, EC., and Aroma.affymetrix, can work with
> CDF only. So after using RMAExpress (in command line mode)  I did get
> Expression matrix out but I could not link 19532 Probeset ids to
> PLANdbAffy annotation csv file to collect gene basic information. What i
> did was , 1st load the full annotation file (not filtered) from
> PLANdbAffy:
> http://affymetrix2.bioinf.fbb.msu.ru/files.html
>
> and search the 2nd colum (Probe_Sets) with ids after RMA and I find 0...
> then i tried the 1st column (the Probes ) and found  8664... but I would
> expect vice versa situation ?
>
>
>
> So Roman can you please:
> 1) advise how to get real ids after RMAExpress run?
> 2) do you plan to build Annotation csv file as Affymetrix dose so that
> other software from Bioconductor oligo  & XPS can use it?
> 3) comment on Christian feedback.
>
>
>
> Btw. Christian, how come RMAExpress, EC., and Aroma.affymetrix can work
> with CDFs only  and oligo & XPS require extra annotation? From what  I
> gather (after peaking into CDF and PGF files ) they show what probes are
> belonging to probe_set. So for probe_set level analysis (or more
> exon_like analysis) the PGF/CLF files alone seem to be enough?
>
>
>
> For bioc list, just to bring attention to this article & DB :
>
>
>
> PLANdbAffy: probe-level annotation database for Affymetrix expression
> microarrays , Ramil N. Nurtdinov1 et al.
>
> http://nar.oxfordjournals.org/content/38/suppl_1/D726.full
>
>
>
> http://affymetrix2.bioinf.fbb.msu.ru/
>
>
>
> Maybe some of bioC experts have comments about it?
>
>
>
> Best,
>
> Branko
>
>
>
> --------------------------
>
> Branislav Misovic,
>
> Department of Toxicogenetics
>
> Leiden University Medical Center
>
> Einthovenweg 20, 2333 ZC Leiden
>
> PO.box 9600, Building2,Room:T3-11
>
> 2300 RC Leiden
>
> The Netherlands
>
> Phone: +31 71 526 9636
>
> Mob: 0653135855
>
> E-mail:
>
> b.misovic at lumc.nl
>
> braniti at gmail.com
>
>
>
>
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>
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