FW: more multtest problems
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@michael-watson-iah-c-378
Last seen 9.6 years ago
Hi Sorry for the re-post! I just could really do with nowing why the p-value from t.test() is different from the rawp value from mt.maxT in multtest, when using the same data and equivalent parameters (see below)! Thanks Mick -----Original Message----- From: michael watson (IAH-C) [mailto:michael.watson@bbsrc.ac.uk] Sent: 11 March 2004 16:17 To: bioconductor@stat.math.ethz.ch Subject: [BioC] more multtest problems Hi Even after some very good help, I am still confused by multtest. Below is the output from my analysis. What I basically do is read in some data, use t.test() to perform a two-tailed, unequal variance t-test on the first row, then use mt.maxT() to perform a t-test on all the rows and then compare the results. What I have found is that although t.test() and mt.maxT() produce the same t value (0.9796), the raw p-values differ (0.3954 vs 0.54285714). Why is rawp from mt.maxT different to the p-value from t.test() Thanks! Mick > library(multtest) > data <- read.table("average.txt", header=TRUE, sep="\t", quote="\"") > cl = c(1,1,1,1,0,0,0) > # do two-tailed t-test, unequal variance > t <- t.test(data[1,1:4],data[1,5:7], alternative="two.sided", var.equal=FALSE) > t Welch Two Sample t-test data: data[1, 1:4] and data[1, 5:7] t = 0.9796, df = 3.199, p-value = 0.3954 alternative hypothesis: true difference in means is not equal to 0 95 percent confidence interval: -2.407296 4.659662 sample estimates: mean of x mean of y 1.130890500 0.004707667 > multt <- mt.maxT(data,cl,test="t",side="abs") We'll do complete enumerations We're doing 35 complete permutations b=1 b=2 b=3 b=4 b=5 b=6 b=7 b=8 b=9 b=10 b=11 b=12 b=13 b=14 b=15 b=16 b=17 b=18 b=19 b=20 b=21 b=22 b=23 b=24 b=25 b=26 b=27 b=28 b=29 b=30 b=31 b=32 b=33 b=34 b=35 > > multt index teststat rawp adjp 1 4 2.4344730 0.02857143 0.02857143 2 3 1.7019798 0.25714286 0.25714286 3 5 1.5719193 0.08571429 0.25714286 4 6 1.3674557 0.02857143 0.25714286 5 2 1.1519341 0.20000000 0.28571429 6 1 0.9796023 0.54285714 0.54285714 _______________________________________________ Bioconductor mailing list Bioconductor@stat.math.ethz.ch https://www.stat.math.ethz.ch/mailman/listinfo/bioconductor
multtest multtest • 814 views
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