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_M ONETARY=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