Hi James,

Your problem lies in the read.affybatch function (ReadAffy is a wrapper of
this).

if you look inside the guts of read.affybatch you'll see where your error is
coming from:


if (dim(pdata)[1] != n) {
        warning("Incompatible phenoData object. Created a new one.\n")
        samplenames <- sub("^/?([^/]*/)*", "", filenames, extended = TRUE)
        pdata <- data.frame(sample = 1:n, row.names = samplenames)
        phenoData <- new("AnnotatedDataFrame", data = pdata,
            varMetadata = data.frame(labelDescription = "arbitrary
numbering",
                row.names = "sample"))
    }



Looks to me like the the phenoData AnnotatedDataFrame is being triggered,
because on isn't supplied it tries to make one. This is then resulting in
substitution being attempted on the list of filenames as it tries to get
something to use as the samplenames. However the error is that it is not
able to use the extended=TRUE. Have a look at the help file for sub function
to see how to setup Perl Compatible Regular Expression on your system
(PCRE).

The regular expressions used are those specified by POSIX 1003.2, either
extended or basic, depending on the value of the extended argument, unless perl
= TRUE when they are those of PCRE, http://www.pcre.org/. (The exact set of
patterns supported may depend on the version of PCRE installed on the system
in use if *R* was configured to use the system PCRE.)

That should hopefully take care of the problem.

Rdgs,
Amos Folarin



---------- Forwarded message ----------
From: "James W. MacDonald" <jmacdon@med.umich.edu>
To: mandova <mandova1005@yahoo.cn>
Date: Wed, 04 Aug 2010 15:33:08 -0400
Subject: Re: [BioC] [R] error with ReadAffy()
 This question is more appropriate for the bioconductor list <
bioconductor@stat.math.ethz.ch>. I have cc'ed there.

Any time you ask a question, you need to give the output of sessionInfo(),
so please give us that output.

Best,

Jim



On 8/4/10 9:08 AM, mandova wrote:

> Hi!I'm doing a little data importing from .cel files,
>
> setwd("/home/mandova/celfiles")
>> mydata<-ReadAffy()
>>
> Error in sub("^/?([^/]*/)*", "", filenames, extended = TRUE) :
>   unused argument(s) (extended = TRUE)
>
>
> Then I tried
>
>> filenames<-paste("GSM",c(seq(138597,138617,1)),".cel",sep="")
>> filenames<-as.character(filenames)
>> filenames
>>
>
> [1] "GSM138597.cel" "GSM138598.cel" "GSM138599.cel" "GSM138600.cel"
>  [5] "GSM138601.cel" "GSM138602.cel" "GSM138603.cel" "GSM138604.cel"
>  [9] "GSM138605.cel" "GSM138606.cel" "GSM138607.cel" "GSM138608.cel"
> [13] "GSM138609.cel" "GSM138610.cel" "GSM138611.cel" "GSM138612.cel"
> [17] "GSM138613.cel" "GSM138614.cel" "GSM138615.cel" "GSM138616.cel"
> [21] "GSM138617.cel"
>
> mydata<-ReadAffy(compress=FALSE,filenames=filenames)
>>
> Error in sub("^/?([^/]*/)*", "", filenames, extended = TRUE) :
>   unused argument(s) (extended = TRUE)
>
> Same error! Could you please help me understand the error message? Thx!!!
>
>
-- 
James W. MacDonald, M.S.
Biostatistician
Douglas Lab
University of Michigan
Department of Human Genetics
5912 Buhl
1241 E. Catherine St.
Ann Arbor MI 48109-5618
734-615-7826

**********************************************************
Electronic Mail is not secure, may not be read every day, and should not be
used for urgent or sensitive issues

	[[alternative HTML version deleted]]

