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---------- Forwarded message ----------
From: Benilton Carvalho
Date: Tuesday, 20 December 2011
Subject: [BioC] problems with pd.genomewidesnp.6
To: Sebastian Thieme <thieme@mi.fu-berlin.de>


My suggestion is to download the annotation file provided by Affymetrix and
check what it provides for the units mentioned below. If it differs from
what is described in the package, I'll be happy to fix it. Otherwise, you
may want to bring this to the attention of the Affymetrix team.

Right now, I'm not able to check this... If this is something you could
check, we would be able to get to an explanation/solution soon. Note that
the pd packages, regarding annotation, are simply a combination of the
CDF/PGF and associated annotation files.

b

On Tuesday, 20 December 2011, Sebastian Thieme <thieme@mi.fu-berlin.de>
wrote:
> Hi at all,
>
> I have some problems with the pd.genomewidesnp.6 package and I hope
> some one can help me. The info with
> get(objects("package:pd.genomewidesnp.6")) is
>
> #Class........: AffySNPCNVPDInfo
> #Manufacturer.: Affymetrix
> #Genome Build.: HG19
> #Chip Geometry: 2572 rows x  2680 columns
>
> I want match the man_festid of each prob to one gene, therefore I look
> in the gene_assoc part and call the gene with minimum distance to the
> respective prob as corresponding gene. My commands for get the raw
> informations are:
>
> snp.f <- dbGetQuery(con6, "select * from featureSet")
> snp.f <-
snpfeature[,c("fsetid","man_fsetid","chrom","physical_pos","strand","cytoband","gene_assoc")]
>
> cn.f <- dbGetQuery(con6, "select * from featureSetCNV")
> cn.f <-
cn.f[,c("fsetid","man_fsetid","chrom","chrom_start","strand","cytoband","gene_assoc")]
>
> snp6.f <- rbind(snp.f,cn.f)
>
> and process the gene_assoc part. Now the problem within the gene_assoc
> part is that there are genes which are not on the same chromosome as
> the respective probs e.g.
>
> fsetid man_fsetid chrom physical_pos strand cytoband
> 650443  CN_618877    12     93793083      -      q22
>                       gene_assoc
> ENST00000358888 // upstream // 315610 // Hs.112553 // RPL41 // 6171
> //ribosomal protein L41 /// ENST00000318066 // downstream // 8981 //
> Hs.524630 // UBE2N // 7334 // ubiquitin-conjugating enzyme E2N (UBC13
> homolog, yeast) /// NR_002212 // exon // 0 // --- // NUDT4P1 // 440672
> // nudix (nucleoside diphosphate linked moiety X)-type motif 4
> pseudogene 1 /// NM_199040 // CDS // 0 // Hs.506325 // NUDT4 // 11163
> // nudix (nucleoside diphosphate linked moiety X)-type motif 4
> ///NM_019094 // CDS // 0 // Hs.506325 // NUDT4 // 11163 // nudix
> (nucleoside diphosphate linked moiety X)-type motif 4
>
> gene "NUDT4P1" is annotated on Chromosome 1 not 12 and this is only
> one. An other example is
>
> fsetid    man_fsetid chrom physical_pos strand cytoband
> 186938 SNP_A-4227519    12     31784081      -   p11.21
>
>                                                     gene_assoc
> ENST00000294419 // upstream // 14576 // Hs.10862 // AK3L1 // 205 //
> adenylate kinase 3-like 1 /// ENST00000412352 // upstream // 16012 //
> Hs.585084 // C12orf72 // 254013 // chromosome 12 open reading frame 72
> /// NM_013410 // upstream // 14564 // Hs.10862 // AK3L1 // 205 //
> adenylate kinase 3-like 1 /// NM_001135864 // upstream // 16012 //
> Hs.585084 // C12orf72 // 254013 // chromosome 12 open reading frame 72
>
> AK3L1 is annotated at chromosome 9 not 12. The corresponding ensembl
> ID (ENST00000294419 ) is mapped to AK4-201 which is annotated on
> chromosome 1 . This are only two examples there are a lot more. Can
> some one help?
>
>
> best regards
>
> Basti
>
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