[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 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.
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.
[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.
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]]
> >
> > __
> > 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
>
__
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
[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
[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
