[BioC] ReadAffy() function

Ron Ophir ron at volcani.agri.gov.il
Tue Feb 2 22:19:29 CET 2010




 
# -----Original Message-----
# From: James W. MacDonald [mailto:jmacdon at med.umich.edu]
# Sent: Tuesday, February 02, 2010 7:22 PM
# To: Ron Ophir
# Cc: bioconductor at stat.math.ethz.ch
# Subject: Re: [BioC] ReadAffy() function
# 
# Hi Ron,
# 
# Ron Ophir wrote:
# > Dear list users,
# >
# >
# >
# > I am running ReadAffy() function under
# >
# >
# >
# > R version 2.10.0 (2009-10-26)
# >
# > i386-pc-mingw32
# >
# >
# >
# > locale:
# >
# > [1] LC_COLLATE=Hebrew_Israel.1255  LC_CTYPE=Hebrew_Israel.1255
# >
# > [3] LC_MONETARY=Hebrew_Israel.1255 LC_NUMERIC=C
# >
# > [5] LC_TIME=Hebrew_Israel.1255
# >
# >
# >
# > attached base packages:
# >
# > [1] stats     graphics  grDevices utils     datasets  methods
# >
# > [7] base
# >
# >
# >
# > other attached packages:
# >
# > [1] RColorBrewer_1.0-2 Heatplus_1.16.0    limma_3.2.1
# >
# > [4] affy_1.24.2        Biobase_2.6.1
# >
# >
# >
# > loaded via a namespace (and not attached):
# >
# > [1] affyio_1.14.0        preprocessCore_1.8.0 tools_2.10.0
# >
# >
# >
# >
# >>From some reason the following code works
# >
# >
# >
# > C.anno = read.delim(file="gal/Citrus.gal",stringsAsFactors=FALSE)
# >
# > targets =
read.delim(file="targets/Targets.txt",stringsAsFactors=FALSE)
# >
# >
# >
# > C.raw =  ReadAffy(filenames = targets$FileName,
# >
# >                   celfile.path = "data",
# >
# >                   sampleNames =
# > paste(targets$Target,targets$Repeat,sep="")
# >
# >   )
# >
# >
# >
# > C.raw at phenoData = new("AnnotatedDataFrame",data = targets)
# >
# > C.raw at featureData = new("AnnotatedDataFrame",data = C.anno)
# >
# >
# >
# > whereas this one
# >
# >
# >
# > C.raw =  ReadAffy(filenames = targets$FileName,
# >
# >                   celfile.path = "data",
# >
# >                   sampleNames =
# > paste(targets$Target,targets$Repeat,sep=""),
# >
# >                   phenoData = new("AnnotatedDataFrame",data =
targets),
# >
# >                   featureData = new("AnnotatedDataFrame",data
=C.anno)
# >
# >   )
# >
# >
# >
# >
# >
# > does not.
# >
# >
# >
# > I get the following error message:
# >
# >
# >
# > Error: the following are not valid files:
# >
# >     data/new("AnnotatedDataFrame", data = C.anno)
# >
# > In addition: Warning message:
# >
# > In AllButCelsForReadAffy(..., filenames = filenames, widget =
widget,  :
# >
# >   sampleNames not same length as filenames. Using filenames as
# > sampleNames instead
# >
# >
# >
# >
# >
# > !! Targets and C.anno are data.frames, since they were read by
# > read.delim() function.
# >
# >
# >
# > Can you think of why is that?
# 
# Sure. You are passing a non-existent argument to a function that has
the
# ellipsis (...) as its first argument. In this case, the ellipsis is
# there to allow ReadAffy() to accept comma-delimited file names.
# 
# What is happening is that featureData = new("AnnotatedDataFrame", data
=
# C.anno) is being parsed and (attempted to be) added to the vector of
# file names. Since the parsed value isn't a valid file you get the
first
# error. Since your sampleNames and filenames are now different, you get
# the second warning.
# 
# Take home lesson: don't add fictitious arguments to ReadAffy().
# 
# Best,
# 
# Jim
# 
#
[Ron Ophir] oops! That's a good idea not to add fictitious arguments to
ReadAffy(). I took it from an old script I wrote. Where I had prepared
new ExpressionSet object - some of the arguments are synonyms and that's
where the mistake come from. It happens. Thanks for the explanation!
R. 
 
# >
# >
# >
# >
# >
# > Thanks,
# >
# > Ron
# >
# >
# >
# >
# >
# >
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# >
# >
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# --
# James W. MacDonald, M.S.
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