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. Dep't. (secretaries) phone:
+64-9-373-7599 ext. 89622
Home phone: +64-9-480-4619
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