The factor names are legal but the Warnings tell you pretty clearly that Car doesn't like such things. So why don't you just use something else that is more conventional.
-- Bert On Sat, Sep 16, 2023 at 1:40 PM 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) > > ``` > > > > sessionInfo() R version 4.3.1 (2023-06-16 ucrt) Platform: > x86_64-w64-mingw32/x64 (64-bit) Running under: Windows 11 x64 (build > 25951) Matrix products: default locale: [1] LC_COLLATE=English_United > States.utf8 LC_CTYPE=English_United States.utf8 > LC_MONETARY=English_United States.utf8 [4] LC_NUMERIC=C > LC_TIME=English_United States.utf8 time zone: America/Chicago tzcode > source: internal attached base packages: [1] stats graphics grDevices > utils datasets methods base other attached packages: [1] car_3.1-2 > carData_3.0-5 tidyr_1.3.0 readr_2.1.4 readxl_1.4.3 ggplot2_3.4.3 > dplyr_1.1.3 loaded via a namespace (and not attached): [1] crayon_1.5.2 > vctrs_0.6.3 cli_3.6.1 rlang_1.1.1 purrr_1.0.2 generics_0.1.3 > labeling_0.4.3 [8] bit_4.0.5 glue_1.6.2 colorspace_2.1-0 hms_1.1.3 > scales_1.2.1 fansi_1.0.4 grid_4.3.1 [15] cellranger_1.1.0 abind_1.4-5 > munsell_0.5.0 tibble_3.2.1 tzdb_0.4.0 lifecycle_1.0.3 compiler_4.3.1 > [22] pkgconfig_2.0.3 rstudioapi_0.15.0 farver_2.1.1 R6_2.5.1 > tidyselect_1.2.0 utf8_1.2.3 parallel_4.3.1 [29] vroom_1.6.3 pillar_1.9.0 > magrittr_2.0.3 bit64_4.0.5 tools_4.3.1 withr_2.5.0 gtable_0.3.4 > > > [[alternative HTML version deleted]] > > ______________________________________________ > R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see > https://stat.ethz.ch/mailman/listinfo/r-help > PLEASE do read the posting guide > http://www.R-project.org/posting-guide.html > and provide commented, minimal, self-contained, reproducible code. > [[alternative HTML version deleted]] ______________________________________________ R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.