[Bioc-devel] [BioC] read.phenoData vs read.AnnotatedDataFrame
huber at ebi.ac.uk
Thu Aug 9 03:12:52 CEST 2007
I am taking this discussion from the main list to bioc-devel. I think
Alice has made a good point in describing a confusing behaviour of
ReadAffy (trying to be smart) that we might want to fix.
Wolfgang Huber EBI/EMBL Cambridge UK http://www.ebi.ac.uk/huber
Johnstone, Alice ha scritto:
> For interest sake, I have found out why I wasn't getting my expected
> results when using read.AnnotatedDataFrame
> Turns out the error was made in the ReadAffy command, where I specified
> the filenames to be read from my AnnotatedDataFrame object. There was a
> typo error with a capital N ($FileName) rather than lowercase n
> ($Filename) as in my target file..whoops. However this meant the
> filename argument was ignored without the error message(!) and instead
> of using the information in the AnnotatedDataFrame object (which
> included filenames, but not alphabetically) it read the .cel files in
> alphabetical order from the working directory - hence the wrong file was
> given the wrong label (given by the order of Annotated object) and my
> comparisons were confused without being obvious as to why or where.
> Our solution: specify that filename is as.character so assignment of
> file to target is correct(after correcting $Filename) now that using
> read.AnnotatedDataFrame rather than readphenoData.
> It may be beneficial to others, that if the filename argument isn't
> specified, that filenames are read from the phenoData object if included
> -----Original Message-----
> From: Martin Morgan [mailto:mtmorgan at fhcrc.org]
> Sent: Thursday, 26 July 2007 11:49 a.m.
> To: Johnstone, Alice
> Cc: bioconductor at stat.math.ethz.ch
> Subject: Re: [BioC] read.phenoData vs read.AnnotatedDataFrame
> Hi Alice --
> "Johnstone, Alice" <Alice.Johnstone at esr.cri.nz> writes:
>> Using R2.5.0 and Bioconductor I have been following code to analysis
>> Affymetrix expression data: 2 treatments vs control. The original
>> code was run last year and used the read.phenoData command, however
>> with the newer version I get the error message Warning messages:
>> read.phenoData is deprecated, use read.AnnotatedDataFrame instead The
>> phenoData class is deprecated, use AnnotatedDataFrame (with
>> ExpressionSet) instead
>> I use the read.AnnotatedDataFrame command, but when it comes to the
>> end of the analysis the comparison of the treatment to the controls
>> gets mixed up compared to what you get using the original
>> read.phenoData ie it looks like the 3 groups get labelled wrong and so
>> the comparisons are different (but they can still be matched up).
>> My questions are,
>> 1) do you need to set up your target file differently when using
>> read.AnnotatedDataFrame - what is the standard format?
> I can't quite tell where things are going wrong for you, so it would
> help if you can narrow down where the problem occurs. I think
> read.AnnotatedDataFrame should be comparable to read.phenoData. Does
> look right? What about
> ? It's not important but pData(pd)$Target is the same as pd$Target.
> Since the analysis is on eset.rma, it probably makes sense to use the
> pData from there to construct your design matrix
> Does design look right?
>> I have three columns sample, filename and target.
>> 2) do you need to use a different model matrix to what I have?
>> 3) do you use a different command for making the contrasts?
> Depends on the question! If you're performing the same analysis as last
> year, then the model matrix and contrasts have to be the same!
>> I have included my code below if that is of any assistance.
>> Many Thanks!
>> ##Read data
More information about the Bioc-devel