[BioC] limma reading genpix files

Bryce MacIver ibm2 at psu.edu
Thu Apr 8 00:19:36 CEST 2004

hello all limma exprts,

I have started using limma to analyse some spotted microarray data 
but have run into problems trying to read the data files in.
 From the limma guide, having specified the "files" ,  then using the command:
  RG<-read.maimages(files, source="genepix")

I get:

Read 7863scan3.gpr
Error in read.table(fullname, skip = skip, header = TRUE, sep = sep, 
as.is = TRUE,  :
	more columns than column names

I have 4 .gpr files that were generated from genepix version 3 with 
7863scan3 being the first

I also tried specifying columns as mentioned in the limma guide:

RG<-read.maimages(files, columns=list(Rf="F635 Median", Gf="F532 
Median", Rb="B635 Median", Gb ="532 Median"))

and got

Error in "[.data.frame"(obj, , columns$Gb) :
	undefined columns selected.

I have no idea how to interpret these error messages and have to say 
that my forays into BioConductor have been a frequent exercise in 
frustration because of constant unintelligible error messages. Could 
some one please help me in solving these issues.

I'm running R 1.8.0 on MacOS X and recently updated limma (1.3?)

	[[alternative HTML version deleted]]

More information about the Bioconductor mailing list