[R] pairwise.t.test vs. t. test
Hi, If I set the p.adjust=none, does it meant that the output p values from the pairwise.t.test will be the same as those from individual t.tests (set var.equal=T, alternative=t)? I actually got different p values from the two tests. See below. Is it supposed to be this way? Thanks Johnny x [1] 61.6 52.7 61.3 65.2 62.8 63.7 64.8 58.7 44.9 57.0 64.3 55.1 50.0 41.0 [15] 43.0 45.9 52.2 45.5 46.9 31.6 40.6 44.8 39.4 31.0 37.5 32.6 23.2 34.6 [29] 38.3 38.1 19.5 21.2 15.8 33.3 28.6 25.8 Grp [1] Yng Yng Yng Yng Yng Yng Yng Yng Yng Yng Yng Yng Med Med Med Med Med Med [19] Med Med Med Med Med Med Old Old Old Old Old Old Old Old Old Old Old Old Levels: Yng Med Old pairwise.t.test(x=x,g=Grp,p.adjust.method=none) Pairwise comparisons using t tests with pooled SD data: x and Grp Yng Med Med 1.0e-06 - Old 2.0e-12 2.6e-05 P value adjustment method: none t.test(x=x[1:12],y=x[25:36],var.equal=T, alternative=t) Two Sample t-test data: x[1:12] and x[25:36] t = 10.5986, df = 22, p-value = 4.149e-10 alternative hypothesis: true difference in means is not equal to 0 95 percent confidence interval: 24.37106 36.22894 sample estimates: mean of x mean of y 59.34167 29.04167 [[alternative HTML version deleted]] __ R-help@stat.math.ethz.ch mailing list 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.
Re: [R] meta characters in file path
Thanks. I tried them, it works for most of those characters except * and ?. Does regular expression work in file names in windows? e.g. I have a machine-generated file named 021706 matrix#1479 @50.csv, of which 1479 is kinda random. Will I be able to match 1479 with some sort of wild card chars? Thanks Johnny -Original Message- From: Tony Plate [mailto:[EMAIL PROTECTED] Sent: Thursday, August 03, 2006 3:42 PM To: Li,Qinghong,ST.LOUIS,Molecular Biology Cc: r-help@stat.math.ethz.ch Subject: Re: [R] meta characters in file path What is the problem you are having? Seems to work fine for me running under Windows2000: write.table(data.frame(a=1:3,b=4:6), file=@# x.csv, sep=,) read.csv(file=@# x.csv) a b 1 1 4 2 2 5 3 3 6 sessionInfo() Version 2.3.1 (2006-06-01) i386-pc-mingw32 attached base packages: [1] methods stats graphics grDevices utils datasets [7] base other attached packages: XML 0.99-8 Li,Qinghong,ST.LOUIS,Molecular Biology wrote: Hi, I need to read in some files. The file names contain come meta characters such as @, #, and white spaces etc, In read.csv, file= option, is there any way that one can make the function to recognize a file path with those characters? Thanks Johnny [[alternative HTML version deleted]] __ R-help@stat.math.ethz.ch mailing list 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. __ R-help@stat.math.ethz.ch mailing list 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.
Re: [R] meta characters in file path
thanks Prof Ripley. dir() returns the path with full names (wildcards replaced) that are exactly what I need. -Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] Behalf Of Prof Brian Ripley Sent: Friday, August 04, 2006 12:27 PM To: Li,Qinghong,ST.LOUIS,Molecular Biology Cc: r-help@stat.math.ethz.ch; Tony Plate Subject: Re: [R] meta characters in file path On Fri, 4 Aug 2006, Li,Qinghong,ST.LOUIS,Molecular Biology wrote: Thanks. I tried them, it works for most of those characters except * and ?. Those are not valid characters in Windows file paths (/ * : ? \ | are invalid in file or dir names). Does regular expression work in file names in windows? No, and I think you may mean wildcards (which is what work on the command line). e.g. I have a machine-generated file named 021706 matrix#1479 @50.csv, of which 1479 is kinda random. Will I be able to match 1479 with some sort of wild card chars? Yes, use dir(), with regexp pattern patching to find the name(s) you want. glob2rx() might be useful here. Thanks Johnny -Original Message- From: Tony Plate [mailto:[EMAIL PROTECTED] Sent: Thursday, August 03, 2006 3:42 PM To: Li,Qinghong,ST.LOUIS,Molecular Biology Cc: r-help@stat.math.ethz.ch Subject: Re: [R] meta characters in file path What is the problem you are having? Seems to work fine for me running under Windows2000: write.table(data.frame(a=1:3,b=4:6), file=@# x.csv, sep=,) read.csv(file=@# x.csv) a b 1 1 4 2 2 5 3 3 6 sessionInfo() Version 2.3.1 (2006-06-01) i386-pc-mingw32 attached base packages: [1] methods stats graphics grDevices utils datasets [7] base other attached packages: XML 0.99-8 Li,Qinghong,ST.LOUIS,Molecular Biology wrote: Hi, I need to read in some files. The file names contain come meta characters such as @, #, and white spaces etc, In read.csv, file= option, is there any way that one can make the function to recognize a file path with those characters? Thanks Johnny [[alternative HTML version deleted]] __ R-help@stat.math.ethz.ch mailing list 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. __ R-help@stat.math.ethz.ch mailing list 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. -- Brian D. Ripley, [EMAIL PROTECTED] Professor of Applied Statistics, http://www.stats.ox.ac.uk/~ripley/ University of Oxford, Tel: +44 1865 272861 (self) 1 South Parks Road, +44 1865 272866 (PA) Oxford OX1 3TG, UKFax: +44 1865 272595 __ R-help@stat.math.ethz.ch mailing list 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. __ R-help@stat.math.ethz.ch mailing list 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.
[R] meta characters in file path
Hi, I need to read in some files. The file names contain come meta characters such as @, #, and white spaces etc, In read.csv, file= option, is there any way that one can make the function to recognize a file path with those characters? Thanks Johnny [[alternative HTML version deleted]] __ R-help@stat.math.ethz.ch mailing list 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.
[R] multinomial test
Hi All, What is the R function for computing multinomial distribution, e.g. f(2,1,3; 2/9, 1/6, 11/18, 6)? That is, a total of 6 trials, event 1's p1=2/9, x1=2, event 2's p2=1/6, x2=1, and event 3's p3=11/18, x3=3. thanks, Johnny [[alternative HTML version deleted]] __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] multinomial test
Thanks Jim. I think my previous posting wasn't clear enough. What I try to do is to compute the probability: f(2,1,3; 2/9, 1/6, 11/18, 6). (If we compute by hand, it is 0.1127). What is the R funtion for doing that? I know for binomial tests, there is a function called binom.test. But for multinomial events, is there a similar function in R? thanks Johnny -Original Message- From: jim holtman [mailto:[EMAIL PROTECTED] Sent: Wednesday, February 22, 2006 5:33 PM To: Li,Qinghong,ST.LOUIS,Molecular Biology Cc: r-help@stat.math.ethz.ch Subject: Re: [R] multinomial test ?sample sample(1:3, 6, TRUE, prob=c(2/9, 1/6, 11/18)) On 2/22/06, Li,Qinghong,ST.LOUIS,Molecular Biology [EMAIL PROTECTED] wrote: Hi All, What is the R function for computing multinomial distribution, e.g. f(2,1,3; 2/9, 1/6, 11/18, 6)? That is, a total of 6 trials, event 1's p1=2/9, x1=2, event 2's p2=1/6, x2=1, and event 3's p3=11/18, x3=3. thanks, Johnny [[alternative HTML version deleted]] __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html -- Jim Holtman Cincinnati, OH +1 513 646 9390 What the problem you are trying to solve? [[alternative HTML version deleted]] __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] multinomial test
Thanks. That is what I try to find. You know what, I have tried ?multinomial,
but it didn't recognize. It is case sensitive I guess.
Johnny
-Original Message-
From: Berton Gunter [mailto:[EMAIL PROTECTED]
Sent: Wednesday, February 22, 2006 5:44 PM
To: 'jim holtman'; Li,Qinghong,ST.LOUIS,Molecular Biology
Cc: r-help@stat.math.ethz.ch
Subject: RE: [R] multinomial test
Qinghong:
R Has an extensive Help system which you should learn to use.
help.search('multinomial')
?Multinomial
Jim: sample() is wrong -- it gives random samples, not probabilities.
-- Bert Gunter
Genentech Non-Clinical Statistics
South San Francisco, CA
-Original Message-
From: [EMAIL PROTECTED]
[mailto:[EMAIL PROTECTED] On Behalf Of jim holtman
Sent: Wednesday, February 22, 2006 3:33 PM
To: Li,Qinghong,ST.LOUIS,Molecular Biology
Cc: r-help@stat.math.ethz.ch
Subject: Re: [R] multinomial test
?sample
sample(1:3, 6, TRUE, prob=c(2/9, 1/6, 11/18))
On 2/22/06, Li,Qinghong,ST.LOUIS,Molecular Biology
[EMAIL PROTECTED] wrote:
Hi All,
What is the R function for computing multinomial distribution, e.g.
f(2,1,3; 2/9, 1/6, 11/18, 6)?
That is, a total of 6 trials, event 1's p1=2/9, x1=2, event
2's p2=1/6,
x2=1, and event 3's p3=11/18, x3=3.
thanks,
Johnny
[[alternative HTML version deleted]]
__
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PLEASE do read the posting guide!
http://www.R-project.org/posting-guide.html
--
Jim Holtman
Cincinnati, OH
+1 513 646 9390
What the problem you are trying to solve?
[[alternative HTML version deleted]]
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[R] write.table call
Hi, I use write.table() to write a file to an external xls file. the column names left-shift one position in output file. I check with col.names() row.names(), the file is fine. How to prevent the shifting? I71 I111I304I307I305I306I114I72 AFFX-BioB-5_at 6.66435 6.7878075.3359625.2501636.47423 5.8821045.9651096.591687195 AFFX-BioB-M_at 6.1632275.9654274.6655692.743531 6.0972445.77137 5.1136836.314003982 Thanks, Johnny [[alternative HTML version deleted]] __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
[R] comment code
Hi All, In R, can one comment out a block of code at once instead of using # one line at a time? Say, in SAS, one can use /**/ to comment out many lines. Thanks, Johnny [[alternative HTML version deleted]] __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
