[BioC] Error by using gpr data with marray

Wolfgang Huber whuber at embl.de
Fri Mar 9 14:52:10 CET 2012

Dear Sandra

in principle, this should work:

  a = ArrayExpress("E-MTAB-109")

I just tried this. An object with data was constructed (a list of 
NChannelSets). However, errors and warnings were thrown. The resulting 
datastructure was more messy than it should be, and the metadata was 
dropped. I'll chase this up with the package maintainer and with the EBI 

You can try to read to the files provided by EBI 'manually' using 
limma's read.maimages etc., but for this you will need to twiddle with 
function call parameters and file formats, and for this you might be 
best off recruiting a local R expert.

	Best wishes

Sandra Heise [guest] scripsit 03/09/2012 11:19 AM:
> hi,
> I am just a beginner in using R and bioconductor. I have a microarray experiment from the arrayexpress database.
> http://www.ebi.ac.uk/arrayexpress/experiments/E-MTAB-109
> 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():
> library(limma)
> library(marray)
> read.GenePix("3088.gpr")
>>   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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Best wishes

Wolfgang Huber

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