[BioC] ExpressionSet class and problems with phenotype and metadata matrices

[Sean MacEachern]

Hello,

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:

>summary(AffyIn)
    lineA.1                 lineB.3
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

>dim(AffyIn)
[1] 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

>dim(AffyPheno)
[1] 7   1

>summary(AffyPheno)
Pheno
 R:4  
 S:3

> all(rownames(AffyPheno) == colnames(AffyIn))
[1] TRUE


#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.

> AffyPheno[c(3,7),c("Pheno")]
[1] R S
Levels: R S

# I was expecting something like the following to be returned:
        Pheno
lineA.3   R
LineB.7   S

#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"))
> metadata
  labelDescrition  rownames
1          Status Phenotype

> phenoData=new("AnnotatedDataFrame", data = AffyPheno, varMetadata = metadata)
> phenoData
An object of class "AnnotatedDataFrame"
  rowNames: line6.1, line6.2, ..., line7.4  (7 total)
  varLabels and varMetadata description:
    Pheno: NA
  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, 

Sean MacEachern

R version 2.6.0 (2007-10-03)
i386-apple-darwin8.10.1
Biobase_1.16.3