[BioC] lumi::lumiR parseColumnName behaves unexpectedly

[Gordon Smyth]

The lumiR() function of the lumi package has an argument 
parseColumnName. According to the documentation, parsing the column 
names (parseColumnName=TRUE) means that the sample column names will 
be retrieved from the BeadStudio data file.

The actual behaviour of the function is the opposite of this when 
then is only one BeadChip in the data file. When there is more than 
one BeadChip, the parseColumnName argument seems to be ignored. Both 
of these behaviours need to be clarified in the documentation.

Gordon

 > library(lumi)
 > y1 <- lumiR(file.path("IlluminaLSK",files[1]),parse=TRUE)
 > sampleNames(y1)
[1] "D" "E" "F"

The column names have been discarded, even though parse=TRUE.

 > y1 <- lumiR(file.path("IlluminaLSK",files[1]),parse=FALSE)
 > sampleNames(y1)
[1] "1735640067_D" "1735640067_E" "1735640067_F"

The column names have been used, even though parse=FALSE.

 > y2 <- lumiR(file.path("IlluminaLSK",files[2]),parse=TRUE)
 > sampleNames(y2)
  [1] "1736925587_A" "1736925587_B" "1736925587_C" "1736925587_D" 
"1736925587_E" "1736925587_F"
  [7] "1736925588_A" "1736925588_B" "1736925588_C" "1736925588_D"

 > y2 <- lumiR(file.path("IlluminaLSK",files[2]),parse=FALSE)
 > sampleNames(y2)
  [1] "1736925587_A" "1736925587_B" "1736925587_C" "1736925587_D" 
"1736925587_E" "1736925587_F"
  [7] "1736925588_A" "1736925588_B" "1736925588_C" "1736925588_D"

For this data set, the value of parseColumnNames makes no difference.

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