[BioC] Error by using gpr data with marray

Sandra Heise [guest] guest at bioconductor.org
Fri Mar 9 11:19:24 CET 2012

I am just a beginner in using R and bioconductor. I have a microarray experiment from the arrayexpress database.


There are given the target txt and row data (gpr). Now i want used
bioconductor to generate a nomalized intensity matrix for all knockout experiments. I thought i have to use limma package and tried to read the data with marray function read.GenePix but there is still an error. Then I tried to read the info txt but there is still an error too. Maybe i just chose the wrong package for my dataset. Unfortunately I don't have a clue how i can generate the normalized datamatrix but the autors of the dataset wrote thez generate the log_fold_change matrix with Imfit limma function. So i thought there is a possibility for me.

please help

 -- output of sessionInfo(): 



>  Error in if (skip > 0L) readLines(file, skip) :
>  missing value where TRUE/FALSE needed

a.target <- read.marrayInfo("E-MTAB-109.sdrf.txt")

>  Error in names(x) <- value : 
>  'names' attribute [30] must be the same length as the vector [7]

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