To whom it may concern,

I am using R 2.9.1 in Linux (Ubuntu - Hardy). I have successfully installed
'affy' and it's dependencies.
I am using a toy array dataset to make sure that I can analyse these arrays
using affy.
The data consists of 15 arrays (GeneChip Human Gene 1.0 ST Arrays).
I have successfully read these arrays into my R workspace (I created the
cdfpackage from the human gene st cdf file from affymetrix using
makecdfenv):

> Data
AffyBatch object
size of arrays=1050x1050 features (10 kb)
cdf=hugenestcdf (33252 affyids)
number of samples=15
number of genes=33252
annotation=hugenestcdf
notes=


I want to be able to create a boxplot and MAplot as described in the 'affy'
primer pdf given on bioconductor (I am able to do this with the Dilution
data provided on bioconductor) but when I try this on my 'Data' I get the
following errors:

> boxplot(Data)
Error in data.frame(log2(intensity(x)[tmp, ])) :
  row names contain missing values
In addition: Warning message:
In data.frame(log2(intensity(x)[tmp, ])) : NAs introduced by coercion
Error in boxplot(data.frame(log2(intensity(x)[tmp, ])), main = main, range =
range,  :
  error in evaluating the argument 'x' in selecting a method for function
'boxplot'

 > MAplot(Data)
Error in .local(object, ...) : subscript out of bounds
In addition: Warning message:
In .local(object, ...) : NAs introduced by coercion


When trying to fitPLM to the data I also get the following error:

> library('affyPLM')
Loading required package: gcrma
Loading required package: matchprobes
Loading required package: splines
Loading required package: preprocessCore

Attaching package: 'affyPLM'


    The following object(s) are masked from package:stats :

     resid,
     residuals,
     weights

> plm.data <- fitPLM(Data)
Error in .local(object, ...) : subscript out of bounds
In addition: Warning message:
In .local(object, ...) : NAs introduced by coercion


I don't know what the errors mean or how to fix the problem so that I can
analyse the data. Can 'affy' be used to analyse the Human Gene 1.0 ST array?


Thank you very much

Cathrine Mitchell

	[[alternative HTML version deleted]]

