[BioC] Create a vector of individual probes to remove from a CDF file

[Jenny Drnevich]

Hi Dana,

RemoveProbes() does not appear to be able to read in a file from the 
working directory, but only an object in your workspace. The object 
probably needs to be a character vector, so try this*:

rejectedprobes <- read.delim("rejectedprobes", as.is=T) [,1]

*This code assumes your data is n rows X 1 column format. Because you 
refers to 'columns in the rejectedprobes file", your data might instead be 
1 row X n columns format. You can check the dimensions of the file thats' 
read in by:

dim(read.delim("rejectedprobes", as.is=T))

If your file is 1 row X n columns, change the [,1] to [1,] to pull out the 
first row instead of the first column. Finally, your file "rejectedprobes" 
is probably really named "rejectedprobes.txt" (Windows likes to hide file 
extensions), so if you're getting an error along the lines of 'unable to 
open connection", the file name is not specified correctly.

Cheers,
Jenny

At 02:33 PM 10/27/2006, Dana Wohlbach wrote:
>Hello,
>I am trying to remove individual probes from analysis by using code
>posted by Ariel Chernomoretz and modified by Jenny Drnevich.   I have
>a list of individual probes that I would like to remove in a tab-
>delimited text file (called rejectedprobes) and the file is in my
>working directory.  The columns in the rejectedprobes file correspond
>to and are named exactly as in the CDF file.  However, when I try to
>use RemoveProbes
>(listOutProbes="rejectedprobes",listOutProbeSets=NULL, cleancdf) as
>directed in the original instructions, it reports the error:
>Error in get(x, envir, mode, inherits) : variable "rejectedprobesat"
>was not found
>I am wondering if anyone can give me some clues as to ways to fix
>this problem.  If you need more information about the problem I'm
>experiencing, please let me know.
>
>Thanks,
>Dana
>
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Jenny Drnevich, Ph.D.

Functional Genomics Bioinformatics Specialist
W.M. Keck Center for Comparative and Functional Genomics
Roy J. Carver Biotechnology Center
University of Illinois, Urbana-Champaign

330 ERML
1201 W. Gregory Dr.
Urbana, IL 61801
USA

ph: 217-244-7355
fax: 217-265-5066
e-mail: drnevich at uiuc.edu