http://www.bioconductor.org/help/course-materials/2009/SeattleNov09/RNASeq/RNASeqTools.pdf
This is the document I found on the web. It is interesting as it has some
functions to perform the Bullard et al. UpperQuartile normalisation. I want
to see how that transforms transcript counts, hence me carrying out the
steps. Typically, just before I get to the interesting bit, it falls down
:-).

To be honest, it would be really cool if a function was written that take a
data frame and upper-quartile normalise the data, using columns as samples
and rows as genes. Have I missed that, does that exist?

head(yAnno)
          ensembl_gene_id ensembl_exon_id chr strand   start     end
gene_biotype
YHR055C.1         YHR055C       YHR055C.1   8     -1  214535  214720
protein_coding
YPR161C.1         YPR161C       YPR161C.1  16     -1  864445  866418
protein_coding
YOL138C.1         YOL138C       YOL138C.1  15     -1   61325   65350
protein_coding
YDR395W.1         YDR395W       YDR395W.1   4      1 1263317 1266151
protein_coding
YGR129W.1         YGR129W       YGR129W.1   7      1  750405  751052
protein_coding
YPR165W.1         YPR165W       YPR165W.1  16      1  875364  875993
protein_coding
The code I am really interested in seeing how works is:

> notZero <- which(rowSums(geneCountsUI) != 0)

> upper.quartiles <- apply(geneCountsUI[notZero,

+ ], 2, function(x) quantile(x, 0.75))

> uq.scaled <- upper.quartiles/sum(upper.quartiles) *

+ sum(laneCounts)
Thanks,

John.

  On Fri, Aug 27, 2010 at 3:21 PM, Kasper Daniel Hansen <
kasperdanielhansen@gmail.com> wrote:

> Inside the function, annoData is just the yAnno data.frame.
>
> The error means that transcript.id - with a default value of
> "ensembl_transcript_id" is not part of the names (colnames) of the
> yAnno object.
>
> At this time you should show us
>  head(yAnno)
> and tell us exactly what document you are following.
>
> Kasper
>
> On Fri, Aug 27, 2010 at 10:03 AM, Johnny H <ukfriend22@googlemail.com>
> wrote:
> > Thanks Kasper for that, the command works but...
> >
> >> yAnnoUI <- makeGeneRepresentation(yAnno, type = "UIgene")
> > Error: transcript.id %in% names(annoData) is not TRUE
> >> annoData
> > Error: object 'annoData' not found
> > Where is annoData coming from?
> >
> > On Fri, Aug 27, 2010 at 2:59 PM, Kasper Daniel Hansen
> > <kasperdanielhansen@gmail.com> wrote:
> >>
> >> This function has been replaced by the more general
> >> makeGeneRepresentation.  So the call would now be
> >>
> >> yAnnoUI <- makeGeneRepresentation(yAnno, type = "UIgene")
> >>
> >> (there are arguments that allow you to set the gene.id and
> >> transcript.id but the defaults are set as below).
> >>
> >> Kasper
> >>
> >> On Fri, Aug 27, 2010 at 9:48 AM, Johnny H <ukfriend22@googlemail.com>
> >> wrote:
> >> > Dear Bioconductors,
> >> > I am using the Genominator library and work through the
> example...until
> >> > I
> >> > get to here
> >> >
> >> >> yAnnoUI <- Genominator:::makeUIgenes(yAnno, gene.id =
> >> >> "ensembl_gene_id",
> >> > transcript.id = "ensembl_transcript_id", verbose = TRUE)
> >> > Error in get(name, envir = asNamespace(pkg), inherits = FALSE) :
> >> >  object 'makeUIgenes' not found
> >> >
> >> > Please can you advise me how I can use the makeUIgenes method?
> >> > Subsequent
> >> > steps in the example don't work without this step.
> >> >
> >> > Thank you.
> >> >
> >> >> sessionInfo()
> >> > R version 2.11.1 (2010-05-31)
> >> > i386-pc-mingw32
> >> > locale:
> >> > [1] LC_COLLATE=English_United Kingdom.1252  LC_CTYPE=English_United
> >> > Kingdom.1252    LC_MONETARY=English_United Kingdom.1252
> >> > LC_NUMERIC=C                            LC_TIME=English_United
> >> > Kingdom.1252
> >> > attached base packages:
> >> > [1] grid      stats     graphics  grDevices utils     datasets
>  methods
> >> > base
> >> > other attached packages:
> >> >  [1] rtracklayer_1.8.1   RCurl_1.4-3         bitops_1.0-4.1
> >> > Genominator_1.2.0   GenomeGraphs_1.8.0  biomaRt_2.4.0
> >> > RSQLite_0.9-2       DBI_0.2-5           ShortRead_1.6.2
> >> > Rsamtools_1.0.8     lattice_0.18-8
> >> > [12] Biostrings_2.16.9   GenomicRanges_1.0.8 IRanges_1.6.15
> >> > yeastRNASeq_0.0.3
> >> > loaded via a namespace (and not attached):
> >> > [1] Biobase_2.8.0   BSgenome_1.16.5 hwriter_1.2     tools_2.11.1
> >> > XML_3.1-1
> >> >
> >> >        [[alternative HTML version deleted]]
> >> >
> >> > _______________________________________________
> >> > Bioconductor mailing list
> >> > Bioconductor@stat.math.ethz.ch
> >> > https://stat.ethz.ch/mailman/listinfo/bioconductor
> >> > Search the archives:
> >> > http://news.gmane.org/gmane.science.biology.informatics.conductor
> >> >
> >
> >
>

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