I don't know if this is a question for Benilton or Martin Morgan (or
someone else?). Anyway, I am getting an error when I try to create a
SnpFeatureSet with some Affy SNP array data. Following is the code and
error:
dat <- read.celfiles(filenames=list.celfiles())
Incompatible phenoData object. Created a new one.
Loading pdmapping50kxba240
Package loaded.
Error in if (!all(featureNames(assayData(object)) ==
featureNames(object))) msg <- paste(msg, :
missing value where TRUE/FALSE needed
14: validityMethod(as(object, superClass))
13: identical(x, TRUE)
12: anyStrings(validityMethod(as(object, superClass)))
11: validObject(.Object)
10: .local(.Object, ...)
9: .nextMethod(.Object, assayData = assayDataNew(storage.mode = "list",
exprs = exprs, sd = sd, npixels = npixels), phenoData =
phenoData,
experimentData = experimentData, annotation = annotation)
8: eval(expr, envir, enclos)
7: eval(call, callEnv)
6: callNextMethod(.Object, assayData = assayDataNew(storage.mode =
"list",
exprs = exprs, sd = sd, npixels = npixels), phenoData =
phenoData,
experimentData = experimentData, annotation = annotation)
5: .local(.Object, ...)
4: initialize(value, ...)
3: initialize(value, ...)
2: new(TheClass, exprs = tmpExprs, sd = tmpSD, npixels = tmpNP,
platform = pkgname, manufacturer = "Affymetrix", phenoData =
tmp$phenoData,
experimentData = tmp$description)
1: read.celfiles(filenames = list.celfiles())
R version 2.4.0 Under development (unstable) (2006-05-01 r37954)
x86_64-unknown-linux-gnu
attached base packages:
[1] "tools" "methods" "stats" "graphics" "grDevices" "utils"
[7] "datasets" "base"
other attached packages:
pdmapping50kxba240 oligo affyio
Biobase
"0.5.0" "0.99.10" "1.1.0"
"1.11.12"
Any takers?
Best,
Jim
James W. MacDonald, M.S.
Biostatistician
Affymetrix and cDNA Microarray Core
University of Michigan Cancer Center
1500 E. Medical Center Drive
7410 CCGC
Ann Arbor MI 48109
734-647-5623
**********************************************************
Electronic Mail is not secure, may not be read every day, and should not be used for urgent or sensitive issues.