[BioC] About beadarray package

[Johnstone, Alice]

Alex,

Try adding in:
sep="," 
To your readBeadSummaryData() command.  I think this should work as the
default separator for this command is "\t", but you are using a *.csv
file.

Cheers 
Alice
________________________________

	From: ssls sddd [mailto:ssls.sddd at gmail.com] 
	Sent: Tuesday, 2 October 2007 5:31 p.m.
	To: Johnstone, Alice
	Cc: bioconductor at stat.math.ethz.ch
	Subject: Re: [BioC] About beadarray package
	
	
	Hi Alice,
	
	I used:
	
	library(beadarray)
	dataFile = "RawData_bkg_092107_Beadarrays.csv"
	BSData <- readBeadSummaryData(dataFile,
ProbeID="TargetID",skip=0,columns = list(exprs = "AVG_Signal", BeadStDev
= "BEAD_STDEV",NoBeads = "Avg_NBEADS")) 
	
	I have attached a snapshot of first few lines of data.
	
	Thanks for the help!
	
	Alex
	
	
	On 10/1/07, Johnstone, Alice < Alice.Johnstone at esr.cri.nz
<mailto:Alice.Johnstone at esr.cri.nz> > wrote: 

		What is the command you are using, and what do the first
few lines of 
		your data file look like?
		
		
		________________________________
		
		        From: ssls sddd [mailto:ssls.sddd at gmail.com]
		        Sent: Tuesday, 2 October 2007 4:01 p.m.
		        To: Johnstone, Alice
		        Cc: bioconductor at stat.math.ethz.ch
		        Subject: Re: [BioC] About beadarray package
		
		
		        The result of sessionInfo () reads as below. But
I think it is 
		up-to-date.
		
		        Thanks!
		
		        Alex
		
		        > sessionInfo()
		        R version 2.5.1 (2007-06-27)
		        i386-pc-mingw32
		
		        locale:
		        LC_COLLATE=English_United States.1252
;LC_CTYPE=English_United
		States.1252;LC_MONETARY=English_United
		States.1252;LC_NUMERIC=C;LC_TIME=English_United
States.1252
		
		        attached base packages:
		        [1] "grid"      "tools"     "stats"
"graphics"  "grDevices" 
		"utils"
		        [7] "datasets"  "methods"   "base"
		
		        other attached packages:
		           beadarray beadarraySNP  quantsmooth
lodplot     quantreg
		SparseM 
		             "1.4.0"      " 1.2.0"      "1.2.0"
"1.1"
		"4.10"       "0.73"
		                affy       affyio  geneplotter
lattice     annotate 
		Biobase
		            "1.14.2"      " 1.4.1"     "1.14.0"
"0.15-11"
		"1.14.1"     "1.14.1"
		               limma
		            "2.10.5"
		
		
		
		        On 10/1/07, Johnstone, Alice
<Alice.Johnstone at esr.cri.nz> wrote:
		
		
		                What version of beadarray are you using?
You might need 
		to update it to
		                the latest version.
		                To ensure you get prompt help your post
needs to include
		the output of:
		
		                sessionInfo()
		
		
		                Cheers 
		                Alice
		
		                > -----Original Message-----
		                > From:
bioconductor-bounces at stat.math.ethz.ch
		                > [mailto:
bioconductor-bounces at stat.math.ethz.ch
		<mailto:bioconductor-bounces at stat.math.ethz.ch> ] On
Behalf Of ssls sddd 
		                > Sent: Tuesday, 2 October 2007 2:43
p.m.
		                > To: bioconductor at stat.math.ethz.ch
		                > Subject: [BioC] About beadarray
package 
		                >
		                > Hello! I tried to read in data using
the function
		                > readBeadSummaryData() but I got the
error message
		like:
		                >
		                > Error in `rownames<-`(`*tmp*`, value =
c(41306L, 
		35002L,
		                > 16863L, 12131L,  :
		                >         attempt to set rownames on
object with no
		dimensions
		                >
		                >
		                > I tried the sample data called
'raw_data.csv' and got 
		quite
		                > similar error
		                > message:
		                >
		                > Error in `rownames<-`(`*tmp*`, value =
c(1L, 2L, 3L,
		4L, 5L,
		                > 6L, 7L, 8L,  : 
		                >         attempt to set rownames on
object with no
		dimensions
		                >
		                >
		                > can anyone suggest how to correct
this?
		                > 
		                > Thank you very much!
		                >
		                > Alex
		                >
		                >       [[alternative HTML version
deleted]]
		                >
		                >
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