Jim,
That works, thanks!
Mark
Mark W. Kimpel, M.D.
-----Original Message-----
From: James W. MacDonald [mailto:jmacdon@med.umich.edu]
Sent: Tuesday, February 07, 2006 11:22 AM
To: Kimpel, Mark William
Cc: Bioconductor Newsgroup
Subject: Re: [BioC] continued problems with ReadAffy
Hi Mark,
I recently fixed read.affybatch() to conform to the new object
checking,
but the fix hasn't propagated to the download server yet.
As a temporary fix, you can load affy and then paste the following
function into your R session (or if you are set up to build from
source,
just replace this function in read.affybatch.R in the source package
and
build the package).
read.affybatch <- function(..., filenames=character(0),
phenoData=new("phenoData"),
description=NULL,
notes="",
compress =
getOption("BioC")$affy$compress.cel,
rm.mask = FALSE, rm.outliers=FALSE,
rm.extra=FALSE,
verbose = FALSE,sd=FALSE, cdfname = NULL)
{
auxnames <- as.list(substitute(list(...)))[-1]
filenames <- .Primitive("c")(filenames, auxnames)
n <- length(filenames)
## error if no file name !
if (n == 0)
stop("No file name given !")
pdata <- pData(phenoData)
##try to read sample names form phenoData. if not there use CEL
filenames
if(dim(pdata)[1] != n) {
##if empty pdata filename are samplenames
warning("Incompatible phenoData object. Created a new one.\n")
samplenames <- sub("^/?([^/]*/)*", "", unlist(filenames),
extended=TRUE)
pdata <- data.frame(sample=1:n, row.names=samplenames)
phenoData <-
new("phenoData",pData=pdata,varLabels=list(sample="arbitrary
numbering"))
}
else samplenames <- rownames(pdata)
if (is.null(description))
{
description <- new("MIAME")
description at preprocessing$filenames <- filenames
description at preprocessing$affyversion <-
library(help=affy)$info[[2]][[2]][2]
}
## read the first file to see what we have
if (verbose) cat(1, "reading",filenames[[1]],"...")
headdetails <- .Call("ReadHeader",filenames[[1]],compress,
PACKAGE="affy")
#print(headdetails)
##now we use the length
dim.intensity <- headdetails[[2]] ##dim(intensity(cel))
##and the cdfname as ref
ref.cdfName <- headdetails[[1]] #cel at cdfName
## allow for non-standard cdfs
if(is.null(cdfname))
cdfname <- ref.cdfName
if (verbose)
cat(paste("instantiating an AffyBatch (intensity a ",
prod(dim.intensity), "x", length(filenames), " matrix)...", sep=""))
if (verbose)
cat("done.\n")
## Change sampleNames to be consistent with row.names of phenoData
object
exprs <- .Call("read_abatch",filenames,compress, rm.mask,
rm.outliers, rm.extra, ref.cdfName,
dim.intensity,verbose, PACKAGE="affy")
colnames(exprs) <- samplenames
#### this is where the code changes from the original
read.affybatch.
#### what we will do here is read in from the 1st to the nth CEL
file
if (!sd){
return(new("AffyBatch",
exprs = exprs,
##se.exprs = array(NaN, dim=dim.sd),
cdfName = cdfname, ##cel at cdfName,
phenoData = phenoData,
nrow = dim.intensity[1],
ncol = dim.intensity[2],
annotation = cleancdfname(cdfname, addcdf=FALSE),
description= description,
notes = notes))
} else {
return(new("AffyBatch",
exprs = exprs,
se.exprs =
.Call("read_abatch_stddev",filenames,compress, rm.mask,
rm.outliers, rm.extra, ref.cdfName,
dim.intensity,verbose, PACKAGE="affy"),
cdfName = cdfname, ##cel at cdfName,
phenoData = phenoData,
nrow = dim.intensity[1],
ncol = dim.intensity[2],
annotation = cleancdfname(cdfname, addcdf=FALSE),
description= description,
notes = notes))
}
}
HTH,
Jim
Kimpel, Mark William wrote:
> After thinking that I had the problem solved, I am continuing to
have
> problems with "ReadAffy". The default options of the function are
still
> leading to the error " sampleNames different from names of phenoData
> rows" and I am unable to figure out its cause. See below for output
and
> sessionInfo(). It appears to me that the samplenames and rownames of
> phenodata are identical and I have used setdiff() to verify this
(output
> is character(0) ).
>
> Ideas? Thanks, Mark
>
>
>>ReadAffy()
>
> Error in validObject(.Object) : invalid class "AffyBatch" object:
> sampleNames different from names of phenoData rows
>
> Enter a frame number, or 0 to exit
>
> 1: ReadAffy()
> 2: read.affybatch(filenames = l$filenames, phenoData = l$phenoData,
> description = l$description, notes = notes, compress = compress, r
> 3: new("AffyBatch", exprs = .Call("read_abatch", filenames,
compress,
> rm.mask, rm.outliers, rm.extra, ref.cdfName, dim.intensity, verb
> 4: initialize(value, ...)
> 5: initialize(value, ...)
> 6: validObject(.Object)
>
> Selection: 2
> Called from: eval(expr, envir, enclos)
> Browse[1]> ls()
> [1] "auxnames" "cdfname" "compress" "description"
> "dim.intensity" "filenames" "headdetails"
> [8] "n" "notes" "pdata" "phenoData"
> "ref.cdfName" "rm.extra" "rm.mask"
> [15] "rm.outliers" "samplenames" "sd" "verbose"
> Browse[1]> samplenames
> [1] "BB01R018.CEL" "BB01R019.CEL" "BB01R020.CEL" "BB01R021.CEL"
> "BB01R022.CEL" "BB01R023.CEL" "BB01R024.CEL" "BB01R025.CEL"
> [9] "BB01R026.CEL" "BB01R027.CEL" "BB01R029.CEL" "BB01R030.CEL"
> "BB01R031.CEL" "BB01R032.CEL" "BB01R033.CEL" "BB01R034.CEL"
> Browse[1]> pdata
> sample
> BB01R018.CEL 1
> BB01R019.CEL 2
> BB01R020.CEL 3
> BB01R021.CEL 4
> BB01R022.CEL 5
> BB01R023.CEL 6
> BB01R024.CEL 7
> BB01R025.CEL 8
> BB01R026.CEL 9
> BB01R027.CEL 10
> BB01R029.CEL 11
> BB01R030.CEL 12
> BB01R031.CEL 13
> BB01R032.CEL 14
> BB01R033.CEL 15
> BB01R034.CEL 16
> Browse[1]> c
>
> Enter a frame number, or 0 to exit
>
> 1: ReadAffy()
> 2: read.affybatch(filenames = l$filenames, phenoData = l$phenoData,
> description = l$description, notes = notes, compress = compress, r
> 3: new("AffyBatch", exprs = .Call("read_abatch", filenames,
compress,
> rm.mask, rm.outliers, rm.extra, ref.cdfName, dim.intensity, verb
> 4: initialize(value, ...)
> 5: initialize(value, ...)
> 6: validObject(.Object)
>
> Selection: 0
>
>>sessionInfo()
>
> Version 2.3.0 Under development (unstable) (2006-01-01 r36947)
> i386-pc-mingw32
>
> attached base packages:
> [1] "tools" "methods" "stats" "graphics" "grDevices"
"utils"
> "datasets" "base"
>
> other attached packages:
> affy Biobase RWinEdt
> "1.9.7" "1.9.6" "1.7-4"
>
> Mark W. Kimpel MD
>
>
>
> Official Business Address:
>
>
>
> Department of Psychiatry
>
> Indiana University School of Medicine
>
> Biotechnology, Research, & Training Center
>
> 1345 W. 16th Street
>
> Indianapolis, IN 46202
>
>
>
> Preferred Mailing Address:
>
>
>
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>
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>
>
>
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>
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>
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--
James W. MacDonald
Affymetrix and cDNA Microarray Core
University of Michigan Cancer Center
1500 E. Medical Center Drive
7410 CCGC
Ann Arbor MI 48109
734-647-5623
