[BioC] [marray] Importing SMD files into marray

Seth Falcon sfalcon at fhcrc.org
Thu Mar 17 16:04:16 CET 2005

Hi Rene,

Could you report back with the version of R and Bioconductor packages
that you are using?  A good way to do this is:


Rene Nederhand <r.nederhand at gmail.com> writes:
>> datadir="~/Desktop"
>> fnames=c("28370.xls")
>> read.SMD(fnames=fnames, path=datadir,DEBUG=TRUE)
> [1] "28370.xls"
> Generating layout from 28370.xls
> [1] "Reading Gal file"
> [1] "done \n "
> Generating target sample info from all files
> [1] "Ch1 Intensity \\(Median\\)"
> Error in file(con, "r") : unable to open connection

A useful thing to do here is call traceback() and post the output.
That can help us help you if we don't immediately recognize the error
condition.  The traceback() function prints out a trace of the
functions that were called up until the error occurred.

> In addition, I tried using the read.SMD2 function that somebody posted
> here a while ago:

I'm not familiar with read.SMD2, but based on the error message:

>> read.SMD2(fnames=fnames, path=datadir,DEBUG=TRUE)
> [1] "~/Desktop/28370.xls"
> [1] NA
> Generating layout from 28370.xls
> Error in if (skip > 0) readLines(file, skip) : 
> 	missing value where TRUE/FALSE needed

What happens if you add skip=0 to the function call?


+ seth

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