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RGLab / flowStats

flowStats: algorithms for flow cytometry data analysis using BioConductor tools
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Error in normalize() #12

Closed niclas-thomas closed 9 years ago

niclas-thomas commented 9 years ago

Attempts to normalize a gating set to one target results in the following error:

my_target_sample <- sampleNames(samples.gating.set)[1] G.norm <- normalize(data=samples.gating.set,target=my_target_sample) Error in (function (classes, fdef, mtable) : unable to find an inherited method for function ‘getGate’ for signature ‘"GatingHierarchy", "numeric"’ In addition: Warning message: In FUN(c("root", "/nonDebris", "/nonDebris/Lymphocytes", "/nonDebris/Lymphocytes/CD3", : NAs introduced by coercion

sessionInfo():

R version 3.1.2 (2014-10-31) Platform: x86_64-redhat-linux-gnu (64-bit)

locale: [1] LC_CTYPE=en_GB.UTF-8 LC_NUMERIC=C LC_TIME=en_GB.UTF-8 LC_COLLATE=en_GB.UTF-8
[5] LC_MONETARY=en_GB.UTF-8 LC_MESSAGES=en_GB.UTF-8 LC_PAPER=en_GB.UTF-8 LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C LC_MEASUREMENT=en_GB.UTF-8 LC_IDENTIFICATION=C

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

other attached packages: [1] openCyto_1.4.0 flowWorkspace_3.12.0 gridExtra_0.9.1 ncdfFlow_2.12.0 BH_1.54.0-5
[6] RcppArmadillo_0.4.500.0 flowViz_1.30.0 lattice_0.20-29 flowCore_1.32.1

loaded via a namespace (and not attached): [1] Biobase_2.26.0 BiocGenerics_0.12.0 chron_2.3-45 clue_0.3-48 cluster_1.15.3
[6] coda_0.16-1 colorspace_1.2-4 corpcor_1.6.7 data.table_1.9.4 DEoptimR_1.0-2
[11] digest_0.6.4 fda_2.4.3 feature_1.2.11 flowClust_3.4.10 flowMeans_1.18.0
[16] flowStats_3.24.0 GGally_0.4.8 ggplot2_1.0.0 graph_1.44.0 gtable_0.1.2
[21] gtools_3.4.1 hexbin_1.27.0 IDPmisc_1.1.17 KernSmooth_2.23-13 ks_1.9.3
[26] latticeExtra_0.6-26 MASS_7.3-35 Matrix_1.1-4 MCMCpack_1.3-3 misc3d_0.8-4
[31] munsell_0.4.2 mvoutlier_2.0.5 mvtnorm_1.0-0 pcaPP_1.9-60 pls_2.4-3
[36] plyr_1.8.1 proto_0.3-10 R.methodsS3_1.6.1 R.oo_1.18.0 R.utils_1.34.0
[41] RBGL_1.42.0 RColorBrewer_1.0-5 Rcpp_0.11.3 reshape_0.8.5 reshape2_1.4
[46] rgl_0.95.1158 Rgraphviz_2.10.0 robCompositions_1.9.0 robustbase_0.91-1 rrcov_1.3-4
[51] scales_0.2.4 sgeostat_1.0-25 stats4_3.1.2 stringr_0.6.2 tcltk_3.1.2
[56] tools_3.1.2 XML_3.98-1.1 zlibbioc_1.12.0

gfinak commented 9 years ago

This is caused by a change in the getGate API that deprecated index references. Somehow.. the normalization code was not updated.

We'll fix it at push the change.

Greg Finak, PhD Staff Scientist Dept. of Biostatistics, Bioinformatics, and Epidemiology Vaccine and Infectious Disease Division Fred Hutchinson Cancer Research Center Seattle, WA On Dec 9, 2014 8:39 AM, "ncthomas" notifications@github.com wrote:

Attempts to normalize a gating set to one target results in the following error:

my_target_sample <- sampleNames(samples.gating.set)[1] G.norm <- normalize(data=samples.gating.set,target=my_target_sample) Error in (function (classes, fdef, mtable) : unable to find an inherited method for function ‘getGate’ for signature ‘"GatingHierarchy", "numeric"’ In addition: Warning message: In FUN(c("root", "/nonDebris", "/nonDebris/Lymphocytes", "/nonDebris/Lymphocytes/CD3", : NAs introduced by coercion

sessionInfo():

R version 3.1.2 (2014-10-31) Platform: x86_64-redhat-linux-gnu (64-bit)

locale: [1] LC_CTYPE=en_GB.UTF-8 LC_NUMERIC=C LC_TIME=en_GB.UTF-8 LC_COLLATE=en_GB.UTF-8

[5] LC_MONETARY=en_GB.UTF-8 LC_MESSAGES=en_GB.UTF-8 LC_PAPER=en_GB.UTF-8 LC_NAME=C

[9] LC_ADDRESS=C LC_TELEPHONE=C LC_MEASUREMENT=en_GB.UTF-8 LC_IDENTIFICATION=C

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

other attached packages: [1] openCyto_1.4.0 flowWorkspace_3.12.0 gridExtra_0.9.1 ncdfFlow_2.12.0 BH_1.54.0-5

[6] RcppArmadillo_0.4.500.0 flowViz_1.30.0 lattice_0.20-29 flowCore_1.32.1

loaded via a namespace (and not attached): [1] Biobase_2.26.0 BiocGenerics_0.12.0 chron_2.3-45 clue_0.3-48 cluster_1.15.3

[6] coda_0.16-1 colorspace_1.2-4 corpcor_1.6.7 data.table_1.9.4 DEoptimR_1.0-2

[11] digest_0.6.4 fda_2.4.3 feature_1.2.11 flowClust_3.4.10 flowMeans_1.18.0

[16] flowStats_3.24.0 GGally_0.4.8 ggplot2_1.0.0 graph_1.44.0 gtable_0.1.2

[21] gtools_3.4.1 hexbin_1.27.0 IDPmisc_1.1.17 KernSmooth_2.23-13 ks_1.9.3

[26] latticeExtra_0.6-26 MASS_7.3-35 Matrix_1.1-4 MCMCpack_1.3-3 misc3d_0.8-4

[31] munsell_0.4.2 mvoutlier_2.0.5 mvtnorm_1.0-0 pcaPP_1.9-60 pls_2.4-3

[36] plyr_1.8.1 proto_0.3-10 R.methodsS3_1.6.1 R.oo_1.18.0 R.utils_1.34.0

[41] RBGL_1.42.0 RColorBrewer_1.0-5 Rcpp_0.11.3 reshape_0.8.5 reshape2_1.4

[46] rgl_0.95.1158 Rgraphviz_2.10.0 robCompositions_1.9.0 robustbase_0.91-1 rrcov_1.3-4

[51] scales_0.2.4 sgeostat_1.0-25 stats4_3.1.2 stringr_0.6.2 tcltk_3.1.2

[56] tools_3.1.2 XML_3.98-1.1 zlibbioc_1.12.0

— Reply to this email directly or view it on GitHub https://github.com/RGLab/flowStats/issues/12.

mikejiang commented 9 years ago

@ncthomas , I've pushed the fix and some enhancements. Also I quickly put together a simple vignette, hope it helps.

niclas-thomas commented 9 years ago

I've tried to install these changes using:

library(devtools) dev_mode() install_github("flowStats",username="RGLab")

and then using the code I used when I reported the error, but I get the same error as above - am I missing something?

mikejiang commented 9 years ago

Make sure your flowStats is 3.25.8

niclas-thomas commented 9 years ago

All works brilliantly now thanks