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@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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