I'm having a little trouble believing what I'm seeing.
To the best of my knowledge,
sample.info <- data.frame( + spl=paste('A', 1:8, sep=''), +
stat=rep(c('cancer' , 'healthy'), each=4))
is not legal R syntax, and R 3.6.1 agrees with me
Error: unexpected '=' in "x <- data.frame(+ spl="
Then I see + c('Sample Name' , 'Cancer
Status')
which R doesn't like either, for obvious reasons.
Error in +c("Sample Name", "Cancer\nStatus") :
invalid argument to unary operator
Are you sure all these + signs are in your actual code?
What do you expect them to do?
On Sat, 20 Jul 2019 at 02:46, Spencer Brackett <
spbracket...@saintjosephhs.com> wrote:
> Sarah,
>
> I am trying to extract phenoData (ie sample information) from the object
> as part of a procedure to analyze my array for probe sets, which I realize
> is under the BioConducter package Biobase and not relevant to this mailing
> list.
>
> Yes the original procedure uses data from the Dilution dataset hosted in
> the AffyBatch package affydata. Previous to this part of the procedure, a
> dataset was create via..
>
> >fake.data <- matrix(rnorm(8*200), ncol=8)
> ##Then phenotype (sample) data was generated in this example through... ##
>
> sample.info <- data.frame( + spl=paste('A', 1:8, sep=''), +
> stat=rep(c('cancer' , 'healthy'), each=4))
>
> ##Then a meta data.frame object was created to give more intelligible
> labels##
>
> > meta.info <- data.frame (labelDescription = + c('Sample Name' , 'Cancer
> Status')) Then we put them all together: > pheno <-
> new("AnnotatedDataFrame", + data = sample.info, + varMetadata = meta.info)
>
> ##Which was then aggregated together##
>
> > pheno <- new("AnnotatedDataFrame", + data = sample.info, + varMetadata =
> meta.info)
>
> >my.experiments <- new("ExpressionSet", + exprs=fake.data,
> phenoData=pheno)
> > my.experiments
> ExpressionSet (storageMode: lockedEnvironment) assayData: 200 features, 8
> samples element names: exprs
>
> ##The following deals with further manipulating the phenoData##
> phenoData
> sampleNames: 1, 2, ..., 8 (8 total) varLabels and varMetadata
> description: spl: Sample Name stat: Cancer Status
>
> featureData
> featureNames: 1, 2, ..., 200 (200 total) fvarLabels and fvarMetadata
> description: none
> experimentData: use 'experimentData(object)'
> Annotation:
>
> ##At this point is when the dataset 'Dilution was read in through
> data(Dilution)
>
> which was made an object of the AnnotatedDataFrame via
>
> >phenoData(Dilution)
>
> My apologies in advance as I know the above info. pertains to functions
> carried out strictly through BioConducor, but is the only context I can
> provide for what I am trying to do.
>
> Best,
>
> Spencer
>
>
> On Fri, Jul 19, 2019 at 10:23 AM Sarah Goslee <sarah.gos...@gmail.com>
> wrote:
>
> > Hi Spencer,
> >
> > Your description doesn't make any sense to me. If anno is already an R
> > object, what are you trying to do with it?
> >
> > data() is for loading datasets that come with packages; if your object
> > is already an R object in your environment, then there's no need for
> > it.
> >
> > It sounds like you are possibly working through an example provided
> > elsewhere, that has sample data loaded with data(). If so, then you do
> > not need that step for your own data. You just need to import it into
> > R in the correct format.
> >
> > If that doesn't help, then I think we need more information on what
> > you're trying to do.
> >
> > Sarah
> >
> > On Fri, Jul 19, 2019 at 10:18 AM Spencer Brackett
> > <spbracket...@saintjosephhs.com> wrote:
> > >
> > > Hello,
> > >
> > > I am trying to create a data set from an object called ‘anno’ in my
> > > environment. I’ve tried arguments like saveRDS(anno, file = “”) and
> > > save(anno, file “.RData”) to save the object as a file to see if that
> > will
> > > work, but it seems for the particular procedure I am trying to carry
> > out, I
> > > need to transpose the object to a data set. Any ideas as to how I might
> > do
> > > this? For reference, my next step in manipulating the data contained in
> > the
> > > object is data(), which evidently does not work for reading in data
> frame
> > > objects as data(“file/object name).
> > >
> > > Best,
> > >
> > > Spencer
> > >
> > > [[alternative HTML version deleted]]
> > >
> > > ______________________________________________
> > > R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see
> > > https://stat.ethz.ch/mailman/listinfo/r-help
> > > PLEASE do read the posting guide
> > http://www.R-project.org/posting-guide.html
> > > and provide commented, minimal, self-contained, reproducible code.
> >
> >
> >
> > --
> > Sarah Goslee (she/her)
> > http://www.numberwright.com
> >
>
> [[alternative HTML version deleted]]
>
> ______________________________________________
> R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see
> https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide
> http://www.R-project.org/posting-guide.html
> and provide commented, minimal, self-contained, reproducible code.
>
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