Dear List, I still having problems in creating a db file for the saureus affy chips. After reading the material and trying and I could not create such files. Can anybody please help me? I am a biologist without much R experience. I have my toptable comparisons but only with the affy probe IDs. Any help would be greatly appreciated. Regards, -- Marcos B. Pinho Instituto Nacional de Câncer - INCA Rio de Janeiro - Brasil [[alternative HTML version deleted]]

Marcos, if I understand your concern, you have used an affy chip for S. aureus and have identified a list of probe names of some interest. You do not know how to resolve the probe names to more biologically meaningful identifiers. There is nothing currently in Bioconductor that solves this problem -- the chip is not widely enough used, it seems. However, from the netaffx resources for this chip, you can obtain a CSV file with annotation. It may not be necessary to build a new annotation package to solve your problem. Simple programming with the annotation table may suffice. Here are some excerpts of explorations of the csv file contents -- I used > dd = read.csv("S_aureus.na32.annot.csv", skip=14, h=TRUE) > dim(dd) [1] 7775 41 > names(dd) [1] "Probe.Set.ID" "GeneChip.Array" [3] "Species.Scientific.Name" "Annotation.Date" [5] "Sequence.Type" "Sequence.Source" [7] "Transcript.ID.Array.Design." "Target.Description" [9] "Representative.Public.ID" "Archival.UniGene.Cluster" [11] "UniGene.ID" "Genome.Version" [13] "Alignments" "Gene.Title" [15] "Gene.Symbol" "Chromosomal.Location" [17] "Unigene.Cluster.Type" "Ensembl" [19] "Entrez.Gene" "SwissProt" [21] "EC" "OMIM" [23] "RefSeq.Protein.ID" "RefSeq.Transcript.ID" [25] "FlyBase" "AGI" [27] "WormBase" "MGI.Name" [29] "RGD.Name" "SGD.accession.number" [31] "Gene.Ontology.Biological.Process" "Gene.Ontology.Cellular.Component" [33] "Gene.Ontology.Molecular.Function" "Pathway" [35] "InterPro" "Trans.Membrane" [37] "QTL" "Annotation.Description" [39] "Annotation.Transcript.Cluster" "Transcript.Assignments" [41] "Annotation.Notes" > table(dd$Gene.Sym) --- Actb ACTB Gapdh GAPDH Hk1 Pcx STAT1 Tfrc 7746 3 3 6 3 3 4 4 3 It seems to me that the most intuitively interesting fields of the table are at best sparsely annotated. You can get the probe sequences from a different bioconductor resource (saureusprobe package) to aid in your own explorations of probe content and context. On Wed, Jan 25, 2012 at 9:44 AM, Marcos Pinho <pinho.microarray at="" gmail.com=""> wrote: > Dear List, > > I still having problems in creating a db file for the saureus affy chips. > After reading the material and trying and I could not create such files. > Can anybody please help me? I am a biologist without much R experience. I > have my toptable comparisons but only with the affy probe IDs. Any help > would be greatly appreciated. > > Regards, > > > -- > Marcos B. Pinho > Instituto Nacional de C?ncer - INCA > Rio de Janeiro - Brasil > > ? ? ? ?[[alternative HTML version deleted]] > > > _______________________________________________ > Bioconductor mailing list > Bioconductor at r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor