[R] summary function did not work with multcomp with 27 comparisons
Michael Dewey
li@t@ @ending from dewey@myzen@co@uk
Sun Nov 11 13:09:10 CET 2018
Dear Richard
If you look in the R-help archives you will find that Gerrit Eichner
suggested that you might need to be more patient. Try using increasing
numbers of comparisons from 4 and plot time taken against n of
comparisons then extrapolate to 27.
Michael
On 11/11/2018 00:51, Friedman, Richard A. wrote:
> Dear List.
>
> I submitted this inquiry on Thursday but it bounced because I wasn;s a memeber under my current e-mail address; I since joined, but did not receive Friday's issue. So
> please excuse me if you have seen this query before.
>
> I ran multcomp with 27 comparisons. 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:
>
> R version 3.5.1 (2018-07-02) -- "Feather Spray"
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> [R.app GUI 1.70 (7543) x86_64-apple-darwin15.6.0]
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> [History restored from /Users/friedman/.Rapp.history]
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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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>
>
>
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--
Michael
http://www.dewey.myzen.co.uk/home.html
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