[BioC] Error with ImaGene out put file in limma

Gordon Smyth smyth at wehi.edu.au
Wed Oct 22 02:51:31 MEST 2003

At 07:34 AM 22/10/2003, Marcelo Luiz de Laia wrote:
>Hi people,
>I execute this step in limma and I have a error below:
> > RegianeSample <-
> > RegianeSample
>   SlideNamber     FileNameCy3    FileNameCy5  Cy3 Cy5
>1           1 lamina1BCYE.txt lamina1XDM.txt BCYE XDM
>2           2 lamina2BCYE.txt lamina2XDM.txt BCYE XDM
>3           3 lamina3BCYE.txt lamina3XDM.txt BCYE XDM
> > slides <- RegianeSample$FileName
> > RG <- read.maimages(slides, source="imagene")
>Error in array(x, c(length(x), 1), if (!is.null(names(x))) list(names(x),  :
>         attempt to set an attribute on NULL
>Our out put file is like this (in the original file, lines not is broken and
>names of fields is separated with tab):
>Field   Meta Row        Meta Column     Row     Column
>XDM/BCYE        1       1       1       1
>Gene ID Flag    Signal Mean     Background Mean
>Cal 1   1       3.5E+16 8.5E+02
>Signal Median   Background Median
>3.6E+04 8.3E+02
>Meta Row range of 1 to 4;
>Meta Column range of 1 to 2
>Row range of 1 to 32;
>Column range of 1 to 24;
>Flag is 1, 2 or 3;
>Please, any tip are welcome and/or one step by step to analyze imagene out
>put file in limma is very apreciate!

The above output does not look like an Imagene output file. Where for 
example are the "Begin Header", "End Header" and "Begin Raw Data" lines? 
Limma can't be expected to find the data without these sign posts. I do not 
have any direct experience with Imagene, but my guess is that you need to 
go back to Imagene and output the data in the raw data format.

A note to everyone: please specify version numbers for limma and R when you 
ask for help.



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