[Bioc-devel] combine sometimes/often fails with LumiBatch objects

[Gordon Smyth]

We've had regular problems with combine() with LumiBatch objects. I 
can't, or don't have time, to provide a reproducible example, but 
here's a recent example from my own practice. I read 5 LumiBatch objects

library(lumi)
x1 <- lumiR(file.path("IlluminaLSK",files[1]))
x2 <- lumiR(file.path("IlluminaLSK",files[2]))
x3 <- lumiR(file.path("IlluminaLSK",files[3]))
x4 <- lumiR(file.path("IlluminaLSK",files[4]))
x5 <- lumiR(file.path("IlluminaLSK",files[5]))

Then

x <- combine(combine(combine(combine(x1,x2),x3),x4),x5)

will fail (return a fatal error), on the final combine. Yet

x <- combine(combine(combine(x2,x3),x4),x5)
x <- combine(x1,x)

will succeed. On the other hand, if I force all the sample names to be unique:

sampleNames(x1) <- pData(x1)$sampleID
sampleNames(x2) <- pData(x2)$sampleID
sampleNames(x3) <- pData(x3)$sampleID
sampleNames(x4) <- pData(x4)$sampleID
sampleNames(x5) <- pData(x5)$sampleID

then

x <- combine(combine(combine(combine(x1,x2),x3),x4),x5)

now works fine.

Hope this provides some useful info.
Gordon


 > library(limma)
 > targets <- readTargets(comment.char="")
 > row.names(targets) <- targets$ArrayID
 > files <- unique(targets$File)
 >
 > library(lumi)
Loading required package: Biobase
Loading required package: tools

Welcome to Bioconductor

   Vignettes contain introductory material. To view, type
   'openVignette()'. To cite Bioconductor, see
   'citation("Biobase")' and for packages 'citation(pkgname)'.

Loading required package: affy
Loading required package: affyio
Loading required package: preprocessCore
Loading required package: mgcv
This is mgcv 1.3-27
Loading required package: annotate
Loading required package: AnnotationDbi
Loading required package: DBI
Loading required package: RSQLite
Loading required package: xtable
 > x1 <- lumiR(file.path("IlluminaLSK",files[1]))
 > x2 <- lumiR(file.path("IlluminaLSK",files[2]))
 > x3 <- lumiR(file.path("IlluminaLSK",files[3]))
 > x4 <- lumiR(file.path("IlluminaLSK",files[4]))
 > x5 <- lumiR(file.path("IlluminaLSK",files[5]))
 >
 > x <- combine(combine(combine(x2,x3),x4),x5)
Warning message:
In combine(combine(combine(x2, x3), x4), x5) :
   Two data sets have some duplicated sample names!
  "_2" were attached to the duplicated sample names!
 > x <- combine(x1,x)
Warning message:
In combine(x1, x) : Two data sets have some duplicated sample names!
  "_2" were attached to the duplicated sample names!
 >
 > pData(x1)
       sampleID label
D 1735640067_D     D
E 1735640067_E     E
F 1735640067_F     F
 > pData(x2)
                  sampleID        label
1736925587_A 1736925587_A 1736925587_A
1736925587_B 1736925587_B 1736925587_B
1736925587_C 1736925587_C 1736925587_C
1736925587_D 1736925587_D 1736925587_D
1736925587_E 1736925587_E 1736925587_E
1736925587_F 1736925587_F 1736925587_F
1736925588_A 1736925588_A 1736925588_A
1736925588_B 1736925588_B 1736925588_B
1736925588_C 1736925588_C 1736925588_C
1736925588_D 1736925588_D 1736925588_D
 > pData(x3)
                  sampleID        label
1736925548_A 1736925548_A 1736925548_A
1736925548_B 1736925548_B 1736925548_B
1736925549_A 1736925549_A 1736925549_A
1736925549_B 1736925549_B 1736925549_B
1736925549_C 1736925549_C 1736925549_C
1736925549_D 1736925549_D 1736925549_D
1736925549_E 1736925549_E 1736925549_E
1736925549_F 1736925549_F 1736925549_F
1736925552_A 1736925552_A 1736925552_A
1736925552_B 1736925552_B 1736925552_B
1736925552_C 1736925552_C 1736925552_C
1736925552_D 1736925552_D 1736925552_D
1736925552_E 1736925552_E 1736925552_E
1736925552_F 1736925552_F 1736925552_F
 > pData(x4)
       sampleID label
C 1897016048_C     C
D 1897016048_D     D
E 1897016048_E     E
F 1897016048_F     F
 > pData(x5)
       sampleID label
D 1897016078_D     D
E 1897016078_E     E
F 1897016078_F     F
 > x <- combine(combine(combine(combine(x1,x2),x3),x4),x5)
Error in combineElement(x[[nm]], y[[nm]]) :
   assayData elements must have identical data
         non-conforming sample(s): D_2, E_2, F_2
In addition: Warning messages:
1: In combine(combine(combine(x1, x2), x3), x4) :
   Two data sets have some duplicated sample names!
  "_2" were attached to the duplicated sample names!
2: In combine(combine(combine(combine(x1, x2), x3), x4), x5) :
   Two data sets have some duplicated sample names!
  "_2" were attached to the duplicated sample names!
 > sampleNames(x1) <- pData(x1)$sampleID
 > sampleNames(x2) <- pData(x2)$sampleID
 > sampleNames(x3) <- pData(x3)$sampleID
 > sampleNames(x4) <- pData(x4)$sampleID
 > sampleNames(x5) <- pData(x5)$sampleID
 >
 > x <- combine(combine(combine(combine(x1,x2),x3),x4),x5)
 > sessionInfo()
R version 2.6.0 (2007-10-03)
i386-pc-mingw32

locale:
LC_COLLATE=English_Australia.1252;LC_CTYPE=English_Australia.1252;LC_MONETARY=English_Australia.1252;LC_NUMERIC=C;LC_TIME=English_Australia.1252

attached base packages:
[1] tools     stats     graphics  grDevices 
utils     datasets  methods   base

other attached packages:
  [1] 
lumi_1.4.0           annotate_1.16.0      xtable_1.5-1 
AnnotationDbi_1.0.0
  [5] 
RSQLite_0.6-3        DBI_0.2-3            mgcv_1.3-27 
affy_1.16.0
  [9] preprocessCore_1.0.0 
affyio_1.6.0         Biobase_1.16.0       limma_2.12.0