Question: Problem with cellHTS2 convertWellCoordinates
0
gravatar for Mark Dane
6.4 years ago by
Mark Dane40
Mark Dane40 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
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ADD COMMENTlink modified 6.4 years ago by Joseph Barry160 • written 6.4 years ago by Mark Dane40
Answer: Problem with cellHTS2 convertWellCoordinates
0
gravatar for Joseph Barry
6.4 years ago by
Joseph Barry160
Dana-Farber Cancer Institute, Boston, USA
Joseph Barry160 wrote:
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
ADD COMMENTlink written 6.4 years ago by Joseph Barry160
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