[BioC] ExpressionSet class and problems with phenotype and metadata matrices
sean.maceach at gmail.com
Thu Feb 28 18:57:31 CET 2008
I'm new to R and Bioconductor. I am trying to analyse a simple microarray
experiment examining two lines: Resistant (R) and susceptible (S) for
differences in expression levels.
The data I have contains a file with expression for 4 and 3 replicates from
the R and S lines respectively. I'm trying to create an ExpressionSet object
to initially complete some exploratory clustering on the data set and I have
been following the vignette " An Introduction to Bioconductor¹s
ExpressionSet Class" by Falcon etal.
I have read in my data:
Min. : 2.0 Min. : 2.0
1st Qu.: 18.0 1st Qu.: 18.0
Median : 38.0 Median : 42.0
Mean : 139.0 Mean : 143.4
3rd Qu.: 96.0 3rd Qu.: 105.0
Max. :6974.0 ...... Max. :7417.0
 38483 7
Following the vignette I have read in a simple phenotype txt file containing
seven rows which relate to the 7 lines with two phenotypes R and S
 7 1
> all(rownames(AffyPheno) == colnames(AffyIn))
#However, it is after this that I start having some problems; as I am using
my own data I have modified some of the exercises in the vignette.
 R S
Levels: R S
# I was expecting something like the following to be returned:
#Also when I try the following command I get this error:
>AffyPheno[AffyPheno$Pheno == "R"]
Error in `[.data.frame`(AffyPheno, AffyPheno$Pheno == "R") :
undefined columns selected
#My R programming knowledge is basic at best so I assumed there was
something wrong there and continued with the metadata and phenoData
> metadata = data.frame(labelDescrition = c("Status"),rownames=c("Phenotype"))
1 Status Phenotype
> phenoData=new("AnnotatedDataFrame", data = AffyPheno, varMetadata = metadata)
An object of class "AnnotatedDataFrame"
rowNames: line6.1, line6.2, ..., line7.4 (7 total)
varLabels and varMetadata description:
additional varMetadata: rownames, labelDescription
# As you can see no error was thrown, but I was expecting something in the
varLabels and varMetadata descrtiptions...
So I thought it was best to check the list to see if anyone could point out
any mistakes I've made before I continue.
While I was here I was also wondering if anyone knew of anything in the
annotation package like the hgu95av2 chip for annotating chicken affy data
in the annotation library?
Thanks in advance,
R version 2.6.0 (2007-10-03)
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