[BioC] Possible Bug in readExpressionSet

[Martin Morgan]

Thanks Tiago for your email.

Please in the future post your questions to the Bioc mailing list
(linked from http://bioconductor.org) so that other may benefit. I've
cc'd that group, and hope that you do not mind.

readExpressionSet requires the name of a file that contains the
'phenoData', i.e., sample descriptions. See the description of this
file by consulting the help file for readExpressionSet:

> library(Biobase)
> ?readExpressionSet

which indicates that the phenoData is read by a function called
read.AnnotatedDataFrame. The example at the bottom of
?readExpressionSet shows how the function should be sued. The help
page for read.AnnotatedDataFrame is accessible at

> ?read.AnnotatedDataFrame

The examples on the read.AnnotatedDataFrame page include a peak at the
first six lines of the sample file, to provide an idea of appropriate
format. The examples can be run with

> example(read.AnnotatedDataFrame)

If you have not already done so, you might look at the vignette 'An
introduction to Biobase and ExpressionSet', accessible with

> openVignette()

Having said all that, I've made a change to the 'devel' version of
Biobase so that only the exprsFile argument is required. This will be
available to users of the development version of R after 12:00 PST
Saturday, or in the next Bioconductor release.

Martin

Tiago Lopes <tiagojab at yahoo.com.br> writes:

> Dear Mr. Morgan
> first of all, I would like to say that I admire and appreciate your work
> towards the creation of useful methods for Bioconductor.
> I just started using it and changed from Matlab and Mathematica to a free and
> open alternative.
> I found the following problems:
>> dataset<-readExpressionSet("small.txt")
> Error in read.table(filename, sep = sep, header = header, quote = quote,  :
>   argument "filename" is missing, with no default
>> dataset<-readExpressionSet("small.txt", exprsArgs=list(sep="\t", quote=""))
> Error in read.table(filename, sep = sep, header = header, quote = quote,  :
>   argument "filename" is missing, with no default
>> dataset<-readExpressionSet("small.txt",
> phenoDataFile=character(0),exprsArgs=list(sep="\t", quote=""))
> Error in file(file, "r") : invalid 'description' argument
> Unfortunately that means for me that I should still use the deprecated version
> of eSet...
> I was in doubt if this was a bug or not, and decided to write, and hope this
> may be useful.
> Kind regards,
> Tiago
> ===========================================
> Tiago Lopes
> "Sprechen Sie langsam, baby. Ich lerne Ihre Sprache !"
> Max-Delbrück Centrum für Molekular Medizin
> Berlin
> ===========================================
>
> ------------------------------------------------------------------------------
>
> Gesendet von [[Yahoo! Mail]].
> Dem pfiffigeren Posteingang.

-- 
Martin Morgan
Computational Biology / Fred Hutchinson Cancer Research Center
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