[BioC] Limma Package to read cDNA data

[Joyce Gu]

Hi Jim,
I followed your instruction, it works.
But,I have another question, since there are 20 lines which I want to skip, I 
tried to use skip=20 during file process or RG process, neither works. Do you 
have any suggestions?
Thank you so much!!
Joyce
>===== Original Message From "James MacDonald" <jmacdon at med.umich.edu> =====
>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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