On Sat, 16 Sep 2023 15:39:49 -0500 Robert Baer <rb...@atsu.edu> wrote:
> When doing Anova using the car package, I get a print warning that > is unexpected. It seemingly involves have my flow cytometry factor > levels named CD271+ and CD171-. But I am not sure this warning > should be intended behavior. Any explanation about whether I'm doing > something wrong? Why can't I have CD271+ and CD271- as factor levels? > Its legal text isn't it? > > library(car) mod = aov(Viability ~ Treatment*Expression, data = dat1) > Anova(mod, type =2) Anova Table (Type II tests) Response: Viability > Sum Sq Df F value Pr(>F) Treatment 19447.3 3 9.2942 0.0002927 *** > Expression 2669.8 1 3.8279 0.0621394 . Treatment:Expression 2226.3 3 > 1.0640 0.3828336 Residuals 16739.3 24 --- Signif. codes: 0 ‘***’ > 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1 Warning messages: 1: In > printHypothesis(L, rhs, names(b)) : one or more coefficients in the > hypothesis include arithmetic operators in their names; the printed > representation of the hypothesis will be omitted 2: In > printHypothesis(L, rhs, names(b)) : one or more coefficients in the > hypothesis include arithmetic operators in their names; the printed > representation of the hypothesis will be omitted 3: In > printHypothesis(L, rhs, names(b)) : one or more coefficients in the > hypothesis include arithmetic operators in their names; the printed > representation of the hypothesis will be omitted > > > The code to reproduce: > > ``` > > > dat1 <-structure(list(Treatment = structure(c(1L, 1L, 1L, 1L, 3L, 1L, > 1L, 1L, 1L, 2L, 2L, > 2L, 2L, 2L, 2L, 2L, 2L, 3L, 3L, 3L, 3L, 3L, > 3L, 3L, 4L, 4L, 4L, > 4L, 4L, 4L, 4L, 4L), levels = c("Control", > "Dabrafenib", "Trametinib", "Combination"), class = "factor"), > Expression = structure(c(2L, 2L, 2L, 2L, 2L, > 1L, 1L, 1L, > 1L, 2L, 2L, 2L, 2L, > 1L, 1L, 1L, 1L, 2L, 2L, 2L, 1L, 1L, 1L, > 1L, 2L, 2L, 2L, 2L, > 1L, 1L, 1L, 1L), levels = c("CD271-", > "CD271+"), class = "factor"), > Viability = c(128.329809725159, > 24.2360176821065, 76.3597924274457, 11.0128771862387, > 21.4683836248318, 140.784162982894, 87.4303286565443, > 118.181818181818, 53.603690178743, > 51.2973284643475, > 5.47760907168941, 27.1574091870075, 50.8360561214684, > 56.5250816836441, > 28.6949836632712, 93.2731116663463, 71.900826446281, > 32.2314049586777, > 24.2360176821065, 27.4649240822602, 24.0822602344801, > 26.542379396502, > 30.693830482414, 27.772438977513, 13.4729963482606, > 8.24524312896406, > 18.5469921199308, 13.9342686911397, 13.3192389006342, > 19.9308091485681, > 17.6244474341726, 16.2406304055353)), > row.names = c(NA, > -32L), > class = c("tbl_df", "tbl", "data.frame")) > > mod = aov(Viability ~ Treatment*Expression, data = dat1) > summary(mod) > library(car) > Anova(mod, type =2) > > ``` There seems to be something wrong in your presentation of the data. When I copied and pasted the code I got an error: > Error: unexpected input in: > "dat1 <-structure(list(Treatment = structure(c(1L, 1L, 1L, 1L, 3L, 1L, > " I don't really understand the provenance of the error, but after some fiddling around I managed to create a structure "dat1": > dput(dat1) > structure(list(Treatment = structure(c(1L, 1L, 1L, 1L, 3L, 1L, > 1L, 1L, 1L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 3L, 3L, 3L, 3L, 3L, > 3L, 3L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L), levels = c("Control", > "Dabrafenib", "Trametinib", "Combination"), class = "factor"), > Expression = structure(c(2L, 2L, 2L, 2L, 2L, 1L, 1L, 1L, > 1L, 2L, 2L, 2L, 2L, 1L, 1L, 1L, 1L, 2L, 2L, 2L, 1L, 1L, 1L, > 1L, 2L, 2L, 2L, 2L, 1L, 1L, 1L, 1L), levels = c("CD271-", > "CD271+"), class = "factor"), Viability = c(128.329809725159, > 24.2360176821065, 76.3597924274457, 11.0128771862387, > 21.4683836248318, 140.784162982894, 87.4303286565443, > 118.181818181818, 53.603690178743, 51.2973284643475, > 5.47760907168941, 27.1574091870075, 50.8360561214684, > 56.5250816836441, 28.6949836632712, 93.2731116663463, > 71.900826446281, 32.2314049586777, 24.2360176821065,> mod = aov(Viability ~ > Treatment*Expression, data = dat1) > summary(mod) > library(car) > Anova(mod, type =2) > 27.4649240822602, 24.0822602344801, 26.542379396502, 30.693830482414, > 27.772438977513, 13.4729963482606, 8.24524312896406, > 18.5469921199308, 13.9342686911397, 13.3192389006342, > 9.9308091485681, 17.6244474341726, 16.2406304055353)), row.names = > c(NA, -32L), class = c("tbl_df", "tbl", "data.frame")) Then doing > mod = aov(Viability ~ Treatment*Expression, data = dat1) > summary(mod) > library(car) > Anova(mod, type =2) produced > Df Sum Sq Mean Sq F value Pr(>F) > Treatment 3 20004 6668 9.553 0.000246 *** > Expression 1 2490 2490 3.568 0.071050 . > Treatment:Expression 3 2386 795 1.140 0.353142 > Residuals 24 16751 698 > --- > Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1 > Anova Table (Type II tests) > > Response: Viability > Sum Sq Df F value Pr(>F) > Treatment 20003.9 3 9.5534 0.0002462 *** > Expression 2490.3 1 3.5679 0.0710500 . > Treatment:Expression 2386.1 3 1.1395 0.3531420 > Residuals 16751.3 24 > --- > Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1 No apparent problems that I can discern. No warnings. cheers, Rolf Turner P.S. > sessionInfo() > R version 4.3.1 (2023-06-16) > Platform: x86_64-pc-linux-gnu (64-bit) > Running under: Ubuntu 22.04.3 LTS > > Matrix products: default > BLAS: /usr/lib/x86_64-linux-gnu/atlas/libblas.so.3.10.3 > LAPACK: /usr/lib/x86_64-linux-gnu/atlas/liblapack.so.3.10.3; LAPACK > version 3.10.0 > > locale: > [1] LC_CTYPE=en_GB.UTF-8 LC_NUMERIC=C > [3] LC_TIME=en_NZ.UTF-8 LC_COLLATE=en_GB.UTF-8 > [5] LC_MONETARY=en_NZ.UTF-8 LC_MESSAGES=en_GB.UTF-8 > [7] LC_PAPER=en_NZ.UTF-8 LC_NAME=C > [9] LC_ADDRESS=C LC_TELEPHONE=C > [11] LC_MEASUREMENT=en_NZ.UTF-8 LC_IDENTIFICATION=C > > time zone: Pacific/Auckland > tzcode source: system (glibc) > > attached base packages: > [1] stats graphics grDevices utils datasets methods base > > > other attached packages: > [1] car_3.0-7 carData_3.0-3 brev_0.0-8 > > loaded via a namespace (and not attached): > [1] compiler_4.3.1 crayon_1.5.2 brio_1.1.3 zip_2.1.1 > [5] Rcpp_1.0.8.3 callr_3.7.3 readxl_1.3.1 > fastmap_1.1.1 [9] R6_2.5.1 openxlsx_4.1.4 curl_5.0.0 > forcats_0.5.0 [13] tibble_3.2.1 desc_1.4.2 > rprojroot_2.0.3 nnet_7.3-19 [17] pillar_1.9.0 rlang_1.1.1 > utf8_1.2.3 testthat_3.1.3 [21] stringi_1.7.8 cachem_1.0.8 > fs_1.6.2 pkgload_1.2.4 [25] eglhmm_0.0-15 > memoise_2.0.1 cli_3.6.1 withr_2.5.0 [29] magrittr_2.0.3 > ps_1.7.5 rio_0.5.29 processx_3.8.1 [33] haven_2.2.0 > hms_1.1.3 remotes_2.4.2 devtools_2.4.2 [37] > lifecycle_1.0.3 vctrs_0.6.2 prettyunits_1.1.1 glue_1.6.2 [41] > data.table_1.12.8 cellranger_1.1.0 sessioninfo_1.2.2 abind_1.4-5 > [45] pkgbuild_1.4.0 fansi_1.0.4 colorspace_1.4-1 > foreign_0.8-79 [49] purrr_0.3.4 pkgconfig_2.0.3 tools_4.3.1 > usethis_2.0.1 [53] ellipsis_0.3.2 R.T. -- Honorary Research Fellow Department of Statistics University of Auckland Stats. 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