[BioC] Limma Package to read cDNA data

[Joyce Gu]

I tried the command to read my .txt file into R for limma analysis, 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'

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