[BioC] Annotation Tools package

[Brad Ander]

Thank you for the help, Alexandre.
That command worked.

We were trying to alter the contents of the myPS variable in the example file
> myPS <- c("117_at", "1007_s_at")

We tried just including as many probesets as possible in the
parentheses, but it was just not working/practical.

When we replaced it with your suggestion of
>allPS<-annotation_HGU133Plus2[,1]
we were able to get the full list of probesets from that column in the
Affy annotation and convert to Entrez gene and then use that list to
get the illumina IDs.

FYI (or anybody's), we were using the following:

Affy Probeset -> Entrez:

annotationFile <- "HG-U133_Plus_2.na29.annot.csv"
dataDirectory <- system.file("data", package = "annotationTools")
annotation_HGU133Plus2 <- read.csv(paste(dataDirectory, annotationFile,
+ sep = "/"), colClasses = "character")
allPS<-annotation_HGU133Plus2[,1]
getANNOTATION(allPS, annotation_HGU133Plus2, diagnose = FALSE,
identifierCol = 1, annotationCol = 19, noAnnotationSymbol = NA,
noAnnotationProvidedSymbol = "---", sep = " /// ")
entrez <- getANNOTATION(allps, annotation_HGU133Plus2, diagnose =
FALSE, identifierCol = 1, annotationCol = 19)
write.matrix(entrez, file = "humanentrez.csv", sep = " ")

Entrez -> illumina:

annotationFileIll <- "HumanRef-8_V3_0_R2_11282963_Ab.csv"
dataDirectory <- system.file("data", package = "annotationTools")
annotation_Illumina <- read.csv(paste(dataDirectory, annotationFileIll,
+ sep = "/"), colClasses = "character")
getANNOTATION(entrez, annotation_Illumina, diagnose = FALSE,
identifierCol = 9, annotationCol = 14, noAnnotationSymbol = NA,
noAnnotationProvidedSymbol = "---", sep = " /// ")
illuminaID <- getANNOTATION(entrez, annotation_Illumina, diagnose =
FALSE, identifierCol = 9, annotationCol = 14)
write.matrix(IlluminaID, file = "illuminaID.csv", sep = " ")


It may not have been the most perfect use of the code but it seems to
work (we are still learning).

Thanks for your help.  If there are any suggestions you feel are
important, please let us know.

Kind regards,
Brad


--
Brad Ander, PhD
M.I.N.D. Institute
University of California at Davis
Room 2434
2805 50th Street
Sacramento, CA  95817



2009/8/10 Alexandre Kuhn <alexandre.kuhn at epfl.ch>
>
> Hi Yingfang,
> Once you have loaded your Affymetrix annotation into R (assume it is
> contained in an R object named 'annot') you could for instance select all
> probe sets by subsetting the data.frame so as to select the first column
>
> > allps<-annot[,1]
>
> I am not sure this answers your question tough. Could you please send some
> lines of code to help me understand what is going wrong?
>
> Best, Alexandre
>
> -----Original Message-----
> From: bioconductor-bounces at stat.math.ethz.ch
> [mailto:bioconductor-bounces at stat.math.ethz.ch] On Behalf Of Yingfang Tian
> Sent: jeudi 6 août 2009 19:23
> To: bioconductor at stat.math.ethz.ch
> Cc: Brad Ander
> Subject: Re: [BioC] Annotation Tools package
>
> Dear Dr Kuhn:
>
> We are Yingfang Tian and Brad Ander from the University of California at
> Davis.  We are working on the cross-platform analysis of 3 platforms:
> llumina Human Ref-8,  Affymetrix U133 plus 2 array, and Affymetrix human
> Exon array.
>
> We are trying to use your annotationTools package in R amd are able to at
> least translate across probes from U133 arrays to Illumina, similar to the
> example you give in the BMC Bioinformatics paper.   We were wondering how to
> import large or entire numbers of probesets into the “myPS” object?  It may
> be a basic R command, but unfortunately we rely on commercial software for
> the majority of our analyses and have limited experience with R (hopefully
> that can change on both fronts).
>
> >From the paper, it seems that we can generate a list of Refseq IDs from
> >the
> Affy Probesets and then use this list (set it as the “myPS” object) to pull
> out the Illumina Probe ID using the refseq column as the identifier column.
> We can export all these with a simple write command.  Right now, we are
> thinking of bridging to/from the Exon arrays with the Unigene.  I guess we
> will have to see how that works
>
> Again, we are having success when dealing with a few probesets, but there
> must be a way to get ALL probesets.  Can you please help us with this?
>  Possibly
> with the example command syntax?  In the paper you mention mapping all the
> mouse probes across platforms, so you must have had to deal with this.
>
> We are likely wanting to try the cross species analysis in the near future
> as well, so learning how to get passed the limit of entering each
> probe/gene/etc manually will be a big help.
>
> Kind regards,
>
> Yingfang and Brad
>
> --
> Yingfang Tian, PhD
> M.I.N.D. Institute
> University of California at Davis
> 2805 50th Street,Room 2434
> Sacramento, CA  95817
> Tel:916-703-0384
>
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>
>