[BioC] Limma Package to read cDNA data

[Gordon Smyth]

At 08:45 AM 5/03/2004, Joyce Gu wrote:
>I tried the command to read my .txt file into R for limma analysis,

What command, exactly?

>  but I got
>the following error message:
>
>Error in file(con, "r") : unable to open connection
>In addition: Warning message:
>cannot open file `os677AT.txt'

This means your data file doesn't exist. Type dir() and if you don't see 
the file, then neither can R. Did you type the name correctly? Do you need 
to specify a path? Do you need to set the working directory?

Gordon

>I could not figure out what's wrong?
>Any suggestion is greatly appreciated!
>
> >===== Original Message From Matthew Ritchie <mritchie at wehi.edu.au> =====
> >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
> >name".
> >
> >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")
> >files
> ># [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
> >example
> >
> >RG <- read.maimages(files, source="genepix")
> >
> >is equivalent to the previous call.  For more information on this
> >function, try
> >
> >?read.maimages
> >
> >or
> >
> >help.start()
> >
> >and take the 'Packages', 'limma' and '3.ReadingData' links.
> >Best wishes,
> >
> >Matt Ritchie