[R] summary function does not work with Westfall correction in multcomp with 27 comparisons

Friedman, Richard A. r@f4 @ending from cumc@columbi@@edu
Thu Nov 8 18:10:50 CET 2018


Dear List.

I ran multcomp with 27 comaprisons. The glht command returned an mcp object,
but the summary command with the Westfall correction ddi not give a summary.
When I ran the same dataset with 4 comparisons I got p-values. When I sued a summary with
univariate or Bonferroni’s method with all 27 comarisons I got p-values. But all 27 did not
work for Wesrfall. Please advise.
Here is a record of my session with 27 comparisons and Westfall:

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objc[31790]: Class FIFinderSyncExtensionHost is implemented in both /System/Library/PrivateFrameworks/FinderKit.framework/Versions/A/FinderKit (0x7fff9c2b7c90) and /System/Library/PrivateFrameworks/FileProvider.framework/OverrideBundles/FinderSyncCollaborationFileProviderOverride.bundle/Contents/MacOS/FinderSyncCollaborationFileProviderOverride (0x119bf8cd8). One of the two will be used. Which one is undefined.
> library(multcomp)
Loading required package: mvtnorm
Loading required package: survival
Loading required package: TH.data
Loading required package: MASS

Attaching package: ‘TH.data’

The following object is masked from ‘package:MASS’:

    geyser

> tumor<-read.table("a8_1wayall_input.txt",sep="\t",header=T)
> class(tumor)
[1] "data.frame"
> dim(tumor)
[1] 309   2
> tumor[1,]
     condition  log2vol
1 aa.vector.4w 7.297375
>
> model<-lm(log2vol~condition,data=tumor)
> summary(model)

Call:
lm(formula = log2vol ~ condition, data = tumor)

Residuals:
   Min     1Q Median     3Q    Max
-7.997 -2.414  0.291  2.164  8.059

Coefficients:
                             Estimate Std. Error t value Pr(>|t|)
(Intercept)                   4.58776    0.60457   7.588  4.3e-13 ***
conditionab.vector.6w         1.39818    0.85499   1.635 0.103054
conditionac.vector.8w         2.89085    0.85499   3.381 0.000820 ***
conditionba.dnmt1kd.4w       -2.67491    0.84733  -3.157 0.001760 **
conditionbb.dnmt1kd.6w       -1.43390    0.84733  -1.692 0.091654 .
conditionbc.dnmt1kd.8w       -0.47188    0.84733  -0.557 0.578020
conditionca.dnmt3bkd.4w      -3.15325    0.89139  -3.537 0.000469 ***
conditioncb.dnmt3bkd.6w      -2.17334    0.89139  -2.438 0.015355 *
conditioncc.dnmt3bkd.8w      -1.50187    0.89139  -1.685 0.093078 .
conditionda.dnmt1kdhrad9.4w   1.08153    1.08991   0.992 0.321863
conditiondb.dnmt1kdhrad9.6w   2.38383    1.08991   2.187 0.029517 *
conditiondc.dnmt1kdhrad9.8w   3.53990    1.08991   3.248 0.001297 **
conditionea.dnmt3bkdhrad9.4w  0.02795    1.06049   0.026 0.978991
conditioneb.dnmt3bkdhrad9.6w  1.34037    1.06049   1.264 0.207263
conditionec.dnmt3bkdhrad9.8w  3.40955    1.06049   3.215 0.001449 **
---
Signif. codes:  0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1

Residual standard error: 3.141 on 294 degrees of freedom
Multiple R-squared:  0.3155, Adjusted R-squared:  0.2829
F-statistic: 9.678 on 14 and 294 DF,  p-value: < 2.2e-16

> model.mc<-glht(model,linfct=mcp(condition=c("ab.vector.6w-aa.vector.4w=0",
+                        "ac.vector.8w-aa.vector.4w=0",
+                        "ac.vector.8w-ab.vector.6w=0",
+       "bb.dnmt1kd.6w-ba.dnmt1kd.4w=0",
+                        "bc.dnmt1kd.8w-ba.dnmt1kd.4w=0",
+                        "bc.dnmt1kd.8w-bb.dnmt1kd.6w=0",
+         "cb.dnmt3bkd.6w-ca.dnmt3bkd.4w=0",
+                        "cc.dnmt3bkd.8w-ca.dnmt3bkd.4w=0",
+                        "cc.dnmt3bkd.8w-cb.dnmt3bkd.6w=0",
+         "db.dnmt1kdhrad9.6w-da.dnmt1kdhrad9.4w=0",
+                        "dc.dnmt1kdhrad9.8w-da.dnmt1kdhrad9.4w=0",
+                        "dc.dnmt1kdhrad9.8w-db.dnmt1kdhrad9.6w=0",
+         "eb.dnmt3bkdhrad9.6w-ea.dnmt3bkdhrad9.4w=0",
+                        "ec.dnmt3bkdhrad9.8w-ea.dnmt3bkdhrad9.4w=0",
+                        "ec.dnmt3bkdhrad9.8w-eb.dnmt3bkdhrad9.6w=0",
+       "ba.dnmt1kd.4w-aa.vector.4w=0",
+                        "ca.dnmt3bkd.4w-aa.vector.4w=0",
+                        "da.dnmt1kdhrad9.4w-ba.dnmt1kd.4w=0",
+                        "ea.dnmt3bkdhrad9.4w-ca.dnmt3bkd.4w=0",
+       "bb.dnmt1kd.6w-ab.vector.6w=0",
+                        "cb.dnmt3bkd.6w-ab.vector.6w=0",
+                        "db.dnmt1kdhrad9.6w-bb.dnmt1kd.6w=0",
+                        "eb.dnmt3bkdhrad9.6w-cb.dnmt3bkd.6w=0",
+       "bc.dnmt1kd.8w-ac.vector.8w=0",
+                        "cc.dnmt3bkd.8w-ac.vector.8w=0",
+                        "dc.dnmt1kdhrad9.8w-bc.dnmt1kd.8w=0",
+                        "ec.dnmt3bkdhrad9.8w-cc.dnmt3bkd.8w=0")))
>
> summary(model.mc,test=adjusted(type="Westfall"))

######################
THE PROGRAM FROZE AT THIS POINT AND DID NOT RETURN ANYTHING
HERE IS MY SESSION INFO

######################

> sessionInfo()
R version 3.5.1 (2018-07-02)
Platform: x86_64-apple-darwin15.6.0 (64-bit)
Running under: macOS High Sierra 10.13.6

Matrix products: default
BLAS: /Library/Frameworks/R.framework/Versions/3.5/Resources/lib/libRblas.0.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/3.5/Resources/lib/libRlapack.dylib

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] stats     graphics  grDevices utils     datasets  methods   base

other attached packages:
[1] multcomp_1.4-8  TH.data_1.0-9   MASS_7.3-50     survival_2.42-6 mvtnorm_1.0-8

loaded via a namespace (and not attached):
[1] zoo_1.8-3        compiler_3.5.1   Matrix_1.2-14    sandwich_2.4-0   codetools_0.2-15 splines_3.5.1    grid_3.5.1       lattice_0.20-35

#############################

Why would the summary function not work with 27 comparisons with Westfall but work with 4 comparisons?
Why would the summary function not work with 27 comparisons with Westfall but work with the same  comparisons with Bonferroni?
Is the problem intrinsic to
A. Westfall’s , method with a large number of comarisons.
B, The impkementation of Westfall’s method in multcomp?
C. Machine requirements for Westfall’s method with so many comparisons?
D. My coding
E. Other.

I have used Westsall;’s method throught the paper which I am now working and would prefer to use it for this
problem for consistency.
I would appreciate any advice.


Thanks and best wishes,
Rich
Richard A. Friedman, PhD
Associate Research Scientist,
Biomedical Informatics Shared Resource
Herbert Irving Comprehensive Cancer Center (HICCC)
Lecturer,
Department of Biomedical Informatics (DBMI)
Room 825
Irving Cancer Research Center
Columbia University Herbert and Florence Irving Medical Center
1130 St. Nicholas Ave
New York, NY 10032
(212)851-4765 (voice)
raf4 using cumc.columbia.edu<mailto:raf4 using cumc.columbia.edu>

http://www.columbia.edu/~raf4/index.html


In memoriam, Steve Ditko


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