[BioC] Problem with cellHTS2 convertWellCoordinates

[Mark Dane]

Hi,

I'm getting the following inconsistent results from cellHTS2 convertWellCoordinates. 

pd <- c("nrow"=108L, "ncol"=36L) 
convertWellCoordinates(c(1, 1500), pd)

correctly returns:

$letnum
[1] "A01"  "AP24"

$let.num
     letters     
[1,] "A"     "01"
[2,] "AP"    "24"

$num
[1]    1 1500


convertWellCoordinates(c(1500, 3888), pd)
 
correctly returns:

$letnum
[1] "AP24" "DD36"

$let.num
     letters     
[1,] "AP"    "24"
[2,] "DD"    "36"

$num
[1] 1500 3888


convertWellCoordinates(c(1, 1500, 3888), pd)

seems to have swapped the first letters on the second and third well names 

$letnum
[1] "A01"  "DP24" "AD36"

$let.num
     letters     
[1,] "A"     "01"
[2,] "DP"    "24"
[3,] "AD"    "36"

$num
[1]    1 1500 3888

I can easily work around this for now but wonder if it causes problems in other routines relying on convertWellCoordinates.

thank you,

Mark Dane
Oregon Health and Sciences University


> sessionInfo()
R version 3.0.0 (2013-04-03)
Platform: x86_64-apple-darwin10.8.0 (64-bit)

locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

attached base packages:
[1] grid      parallel  stats     graphics  grDevices utils     datasets  methods  
[9] base     

other attached packages:
[1] cellHTS2_2.24.0    locfit_1.5-9.1     hwriter_1.3        vsn_3.28.0        
[5] splots_1.26.0      genefilter_1.42.0  Biobase_2.20.0     BiocGenerics_0.6.0
[9] RColorBrewer_1.0-5

loaded via a namespace (and not attached):
 [1] affy_1.38.1           affyio_1.28.0         annotate_1.38.0      
 [4] AnnotationDbi_1.22.5  BiocInstaller_1.10.1  Category_2.26.0      
 [7] DBI_0.2-6             graph_1.38.0          GSEABase_1.22.0      
[10] IRanges_1.18.0        lattice_0.20-15       limma_3.16.3         
[13] MASS_7.3-26           prada_1.36.0          preprocessCore_1.22.0
[16] RBGL_1.36.2           robustbase_0.9-7      rrcov_1.3-3          
[19] RSQLite_0.11.3        splines_3.0.0         stats4_3.0.0         
[22] survival_2.37-4       tools_3.0.0           XML_3.95-0.2         
[25] xtable_1.7-1          zlibbioc_1.6.0