[BioC] Limma Package to read cDNA data

[James MacDonald]

You did not have the file in your current directory. To set your
directory, you have to use setwd(). What you did was just find the name
of a file in a particular directory.

Try

setwd("D:/BioconductorProject/OScaseAnalysis")
file <- list.files(pattern="\\.txt")

and then proceed with your analysis.

Best,

Jim



James W. MacDonald
Affymetrix and cDNA Microarray Core
University of Michigan Cancer Center
1500 E. Medical Center Drive
7410 CCGC
Ann Arbor MI 48109
734-647-5623

>>> Joyce Gu <jwgu at bcm.tmc.edu> 03/05/04 10:28AM >>>
Hi,
I did have my file in R environment, first I use this command to get my
file 
into my current directory,
>
file<-dir(path="D:/BioconductorProject/OScaseAnalysis",pattern="*.txt")
and I check it is there,
> file
[1] "os677AT.txt"
then I used the following command to read my data into R
RG<-read.maimages(file,columns=list(Rf="Ch2 Median",Rb="Ch2 B
Median",Gf="Ch1 
Median",Gb=" Ch1 B Median"))
Unfortunately, I got the following error message,
Error in file(con, "r") : unable to open connection
In addition: Warning message: 
cannot open file `os677AT.txt'

The file os677AT.txt is there, why they still can not find them.
Thanks

>===== Original Message From Gordon Smyth <smyth at wehi.edu.au> =====
>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

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