[BioC] File format for single channel analysis of Agilent microarray data with Limma?

Parisa [guest] guest at bioconductor.org
Wed May 23 15:50:40 CEST 2012


I am following the protocol outlined here for analysis of single channel Agilent microarray data: 


I keep getting the following error message when using Limma's read.maimages function to load my data into an RGList object: 

Error in RG[[a]][, i] <- obj[, columns[[a]]] :
  number of items to replace is not a multiple of replacement length 

I think this may be due to my Agilent raw data txt files being in the wrong format. I am having difficulty finding an example Agilent feature extraction raw data txt file online to compare it to. A link to a screen shot of one of the files I am using is below. I would appreciate if someone could let me know if it is in the correct format, and if not then what format it should be in to prevent the above error message from coming up. 

Thank you,



 -- output of sessionInfo(): 

> sessionInfo()R version 2.13.1 (2011-07-08)
Platform: x86_64-apple-darwin9.8.0/x86_64 (64-bit)

[1] en_GB.UTF-8/en_GB.UTF-8/C/C/en_GB.UTF-8/en_GB.UTF-8

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
[1] limma_3.8.3

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