[BioC] Problem with cellHTS2 convertWellCoordinates

[Joseph Barry]

Dear Mark,

Thanks for your continued input. This is indeed a bug that we have now fixed!

A while back I extended the alphanumeric notation of the cellHTS2 package to the range A,B,…,Z,AA,AB,…,ZZ for the alpha part of the well ids. This was driven by the need to support larger well plates, and for the standard well formats (96,384,1536 etc.) we have not had any problems or received any bug reports from users (I have yet to see the alpha id go above AF). As a result of this, a subtle bug in the getAlphaNumeric() function remained undetected as the function still returned correct annotation for the smaller, standard formats. I should have been more careful to perform more exhaustive testing of larger, more exotic plate formats.

In any case, I have now committed the bug-fix to cellHTS2-devel and confirmed that it corrects the error that you report.

Best wishes,
Joseph Barry

On May 10, 2013, at 7:56 PM, Mark Dane wrote:

> 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 
> _______________________________________________
> Bioconductor mailing list
> Bioconductor at r-project.org
> https://stat.ethz.ch/mailman/listinfo/bioconductor
> Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor