[BioC] Limma Package to read cDNA data

Matthew Ritchie mritchie at wehi.edu.au
Fri Feb 27 05:18:59 MET 2004

Hi Joyce,

The function read.maimages() should be able to handle your custom format 
data.  You can specify the columns you want to read in for the red 
foreground and background (Rf, Rb) and green foreground and background 
(Gf, Gb) using the 'columns' argument, which takes a list with 
components Rf="red foreground column name", Gf="green foreground column 
name", Rb="red background column name" and Gb="green background column 

For example, if I have 2 image analysis output files (array1.txt and 
array2.txt in tab delimited text format) in the current working 
directory, and I want the columns "F635 Mean" and "F532 Mean" for the 
red and green foregrounds and "B635 Median" and "B532 Median" for the 
red and green backgrounds, then the following commands:

files <- dir(pattern=".txt")
# [1] "array1.txt" "array2.txt"
RG <- read.maimages(files, columns=list(Rf="F635 Mean", Rb="B635 
Median", Gf="F532 Mean", Gb="B532 Median"))

will read in the relevant columns and store them in an RGList object. 
 Alternatively, if your image analysis data is from one of the packages 
Spot, GenePix, SMD, Imagene, Arrayvision or Quantarray, then you can 
specify this using the 'source' argument.  The relevant columns (Rf, Rb, 
Gf and Gb) are extracted automatically when 'source' is specified.  For 

RG <- read.maimages(files, source="genepix")

is equivalent to the previous call.  For more information on this 
function, try




and take the 'Packages', 'limma' and '3.ReadingData' links.
Best wishes,

Matt Ritchie
PhD Student
Division of Genetics and Bioinformatics
The Walter and Eliza Hall Institute of Medical Research
1G Royal Parade
Parkville, 3050 VIC AUSTRALIA
email: mritchie at wehi.edu.au
web: http://bioinf.wehi.edu.au
Joyce Gu wrote:

>Hello everyone,
>I tried to use limma package to read cDNA data into R, I tried the samples 
>swirl, it all works, but my cDNA data is not the same as the sample data, my 
>data is tab-delimited .txt file, the header information is different from the 
>sample provided, I am wondering is any way I can manupiated the function to be 
>able to read customed data format with limma package, like pick up 
>colume="string", just as read.marrayRaw()?
>Any idea is greatly appreciated!
>Joyce Gu   M.S.
>Scientific Programmer
>Cancer Genomics Group
>Baylor College of Medicine 
>Phone: 832-824-4680
>Fax: 832-825-4038

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