[BioC] readBeadSummaryData problem- duplicate row name error

[Johnstone, Alice]

Hi Peter

To make sure you are using the correct version of beadarray you should
install it with the following command:
source("http://bioconductor.org/biocLite.R")
biocLite("beadarray") 

That will avoid the error you are getting with it being built with
2.7.0.

as for the duplicate row.names error, what do the first 10 lines of your
data file look like?


Cheers
Alice


-----Original Message-----
From: bioconductor-bounces at stat.math.ethz.ch
[mailto:bioconductor-bounces at stat.math.ethz.ch] On Behalf Of Keyel,
Peter
Sent: Tuesday, 8 April 2008 9:54 a.m.
To: bioconductor at stat.math.ethz.ch
Subject: [BioC] readBeadSummaryData problem- duplicate row name error

Hello,

I'm having difficulty reading beadsummary data into R (2.6.2)with
beadarray 1.7.8. I'm getting an error about duplicate row names
regardless of what I set the ProbeID to. I checked the ProbeID column
for duplicates, and there are none. I also tried creating a new column
that only contained the row number and still got the same error when I
used that. When I load beadarray 1.7.8, I get a warning that it was
built with 2.7.0, so I downloaded an alpha version of 2.7.0 and tried
that. Still the same error. How do I persuade it to read my data? What
am I doing wrong?

Thanks,
Peter

Here is what I put into R (2.6.2) and the output, trying to set the
ProbeID to different things. The sessionInfo file follows.

> BSData = readBeadSummaryData(dataFile, sampleSheet=sampleSheet, sep 
> =",",
+ skip =7, columns = list(exprs ="AVG_Signal", se.exprs="BEAD_STDERR", 
+ NoBeads = "Avg_NBEADS", Detection = "Detection PVal"))

Error in read.table(as.character(dataFile), sep = sep, header = TRUE,  :

  duplicate 'row.names' are not allowed

> BSData = readBeadSummaryData(dataFile, sampleSheet=sampleSheet, sep 
> =",",
+ skip =7, columns = list(exprs ="AVG_Signal", se.exprs="BEAD_STDERR", 
+ NoBeads = "Avg_NBEADS", Detection = "Detection PVal"), 
+ ProbeID="ProbeID")

Error in read.table(as.character(dataFile), sep = sep, header = TRUE,  :

  duplicate 'row.names' are not allowed

> BSData = readBeadSummaryData(dataFile, sampleSheet=sampleSheet, sep 
> =",",
+ skip =7, columns = list(exprs ="AVG_Signal", se.exprs="BEAD_STDERR", 
+ NoBeads = "Avg_NBEADS", Detection = "Detection PVal"), 
+ ProbeID="TargetID")

Error in read.table(as.character(dataFile), sep = sep, header = TRUE,  :

  duplicate 'row.names' are not allowed

> BSData = readBeadSummaryData(dataFile, sampleSheet=sampleSheet, sep 
> =",",
+ skip =7, columns = list(exprs ="AVG_Signal", se.exprs="BEAD_STDERR", 
+ NoBeads = "Avg_NBEADS", Detection = "Detection PVal"), 
+ ProbeID="SYMBOL")

Error in read.table(as.character(dataFile), sep = sep, header = TRUE,  :

  duplicate 'row.names' are not allowed

> sessionInfo()

R version 2.6.2 (2008-02-08)
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] tools     stats     graphics  grDevices utils     datasets  methods

[8] base     

other attached packages:
 [1] beadarray_1.7.8      affy_1.16.0          preprocessCore_1.0.0
 [4] affyio_1.6.1         geneplotter_1.16.0   lattice_0.17-4      
 [7] annotate_1.16.1      xtable_1.5-2         AnnotationDbi_1.0.6 
[10] RSQLite_0.6-7        DBI_0.2-4            Biobase_1.16.3      
[13] limma_2.9.17        

loaded via a namespace (and not attached):
[1] grid_2.6.2         KernSmooth_2.22-22 RColorBrewer_1.0-2

------------------------------------------------------------------------
-----
-------
This is the relevant R information using 2.7.0 alpha:

> BSData = readBeadSummaryData(dataFile, sampleSheet = sampleSheet, sep
> =",",
+ header=TRUE, skip = 7, columns = list(exprs="AVG_Signal", se.exprs = 
+ "BEADSTDERR", NoBeads = "Avg_NBEADS", Detection = "Detection
PVal",
+ ), ProbeID ="ProbeID")

Error in read.table(as.character(dataFile), sep = sep, header = TRUE,  :

  duplicate 'row.names' are not allowed

> BSData = readBeadSummaryData(dataFile, sampleSheet = sampleSheet, sep
> =",",
+ header=TRUE, skip = 7, columns = list(exprs="AVG_Signal",  se.exprs = 
+ "BEADSTDERR", NoBeads = "Avg_NBEADS",  Detection = "Detection PVal"))

Error in read.table(as.character(dataFile), sep = sep, header = TRUE,  :

  duplicate 'row.names' are not allowed

> sessionInfo()
R version 2.7.0 alpha (2008-04-04 r45088)
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] tools     stats     graphics  grDevices utils     datasets  methods 
[8] base     

other attached packages:
 [1] beadarray_1.7.8      affy_1.16.0          preprocessCore_1.0.0
 [4] affyio_1.6.1         geneplotter_1.16.0   lattice_0.17-6      
 [7] annotate_1.16.1      xtable_1.5-2         AnnotationDbi_1.0.6 
[10] RSQLite_0.6-8        DBI_0.2-4            Biobase_1.16.3      
[13] limma_2.12.0        

loaded via a namespace (and not attached):
[1] grid_2.7.0         KernSmooth_2.22-22 RColorBrewer_1.0-2


Peter Keyel, PhD
postdoctoral research associate
Howard Hughes Medical Institute
Rheumatology Division
Washington University Medical Center

314-747-1071
pkeyel2 at im.wustl.edu

"He fought the cause of man
Many people loved his courage
Many followed his command
He changed the old into the new
And the course of things to come"
-Kansas, "Closet Chronicles"


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