[R] how to aggregate T-test result in an elegant way?
Yao He
yao.h.1988 at gmail.com
Tue Jan 8 00:31:07 CET 2013
Yes, thanks a lot for your help!
Regards
2013/1/8 arun <smartpink111 at yahoo.com>:
> Hi Yao,
>
> You could also have the results in a wide format:
> res<-do.call(rbind,lapply(lapply(split(b,b$variable),function(x) t.test(x$value[x$O2=="13%"],x$value[x$O2=="21%"])),function(x) data.frame(mean13=x$estimate[1],mean21=x$estimate[2],p.value=x$p.value,CILow=x$conf.int[1],CIHigh=x$conf.int[2])))
> res
> # mean13 mean21 p.value CILow CIHigh
> #EMW 14.35000 17.68000 0.09355374 -7.682686 1.022686
> #EW.17.5 42.87000 45.97333 0.17464018 -9.265622 3.058955
> #EW.INCU 49.61333 47.08333 0.43689727 -7.119234 12.179234
> A.K.
>
>
>
>
> ----- Original Message -----
> From: Yao He <yao.h.1988 at gmail.com>
> To: arun <smartpink111 at yahoo.com>
> Cc: R help <r-help at r-project.org>
> Sent: Monday, January 7, 2013 10:57 AM
> Subject: Re: [R] how to aggregate T-test result in an elegant way?
>
> Hi,arun
>
> Yes , I just want to do the t.test
> I think maybe it is not necessary to generate a 3D array from the raw
> data.frame by acast() at first
>
> Thanks a lot
>
> 2013/1/7 arun <smartpink111 at yahoo.com>:
>> Hi Yao,
>>
>> It's okay.
>>
>> How did you generate the 3 D array?
>> Using ?acast()
>>
>> I am not sure I understand your question "
>>
>> if you meet a t-test task as I described , is that generate a
>> high-dimension array a good way ?"
>>
>> Do you want to do the t-test in the melt dataset?
>>
>> b<- read.table(text="
>> ID O2 variable value
>> 1 TWF2H5 13% EW.INCU 49.38
>> 2 TWF2H6 13% EW.INCU 48.02
>> 3 TWF2H19 13% EW.INCU 51.44
>> 280 TWF2H101 13% EW.17.5 42.26
>> 281 TWF2H105 13% EW.17.5 43.52
>> 282 TWF2H106 13% EW.17.5 42.83
>> 472 TWF2N102 21% EW.17.5 45.97
>> 473 TWF2N104 21% EW.17.5 43.32
>> 474 TWF2N106 21% EW.17.5 48.63
>> 689 TWF2N2 21% EMW 19.57
>> 690 TWF2N6 21% EMW 18.07
>> 691 TWF2N10 21% EMW 15.4
>> 491 TWF2H5 13% EMW 15.61
>> 492 TWF2H6 13% EMW 13.41
>> 493 TWF2H19 13% EMW 14.03
>> 199 TWF2N2 21% EW.INCU 48.69
>> 200 TWF2N6 21% EW.INCU 50.52
>> 201 TWF2N10 21% EW.INCU 42.04
>> ",sep="",header=TRUE,stringsAsFactors=FALSE)
>> res<-lapply(lapply(split(b,b$variable),function(x) t.test(x$value[x$O2=="13%"],x$value[x$O2=="21%"])),function(x) data.frame(mean=x$estimate,p.value=x$p.value))
>> res1<-do.call(rbind,res)
>> row.names(res1)[grep("mean of x",row.names(res1))]<-gsub("(.*\\.).*$","\\113%",row.names(res1)[grep("mean of x",row.names(res1))])
>> row.names(res1)[grep("mean of y",row.names(res1))]<-gsub("(.*\\.).*$","\\121%",row.names(res1)[grep("mean of y",row.names(res1))])
>> res1
>> # mean p.value
>> #EMW.13% 14.35000 0.09355374
>> #EMW.21% 17.68000 0.09355374
>> #EW.17.5.13% 42.87000 0.17464018
>> #EW.17.5.21% 45.97333 0.17464018
>> #EW.INCU.13% 49.61333 0.43689727
>> #EW.INCU.21% 47.08333 0.43689727
>>
>> A.K.
>>
>>
>>
>> ----- Original Message -----
>> From: Yao He <yao.h.1988 at gmail.com>
>> To: arun <smartpink111 at yahoo.com>
>> Cc: R help <r-help at r-project.org>
>> Sent: Monday, January 7, 2013 4:00 AM
>> Subject: Re: [R] how to aggregate T-test result in an elegant way?
>>
>> Hi, arun
>> I'm so sorry for that isn't helpful.
>> One of question is that I don't know how to subset a small part as it
>> is a 3-dimension array so I just show the structure of that.
>> I tried dput() to a file , then what should I do for subsetting it?
>>
>> Another question is :
>> My rawdata is a "melt" dataframe like that:
>> IID O2 variable value
>> 1 TWF2H5 13% EW.INCU 49.38
>> 2 TWF2H6 13% EW.INCU 48.02
>> 3 TWF2H19 13% EW.INCU 51.44
>> 280 TWF2H101 13% EW.17.5 42.26
>> 281 TWF2H105 13% EW.17.5 43.52
>> 282 TWF2H106 13% EW.17.5 42.83
>> 472 TWF2N102 21% EW.17.5 45.97
>> 473 TWF2N104 21% EW.17.5 43.32
>> 474 TWF2N106 21% EW.17.5 48.63
>> 689 TWF2N2 21% EMW 19.57
>> 690 TWF2N6 21% EMW 18.07
>> 691 TWF2N10 21% EMW 15.4
>> 491 TWF2H5 13% EMW 15.61
>> 492 TWF2H6 13% EMW 13.41
>> 493 TWF2H19 13% EMW 14.03
>> 199 TWF2N2 21% EW.INCU 48.69
>> 200 TWF2N6 21% EW.INCU 50.52
>> 201 TWF2N10 21% EW.INCU 42.04
>>
>> if you meet a t-test task as I described , is that generate a
>> high-dimension array a good way ?
>> Thank you!
>>
>> Yao He
>> 2013/1/7 arun <smartpink111 at yahoo.com>:
>>> HI,
>>> I tried to create an example dataset (as you didn't provide the data).
>>> set.seed(25)
>>> a<-array(sample(1:50,60,replace=TRUE),dim=c(2,10,3))
>>> dimnames(a)[[1]]<-c("13%","21%")
>>> dimnames(a)[[2]]<-paste("TWF2H",101:110,sep="")
>>> dimnames(a)[[3]]<-c("EW.INCU","EW.17.5","EMW")
>>>
>>>
>>> str(a)
>>> # int [1:2, 1:10, 1:3] 21 35 8 45 7 50 32 17 4 15 ...
>>> #- attr(*, "dimnames")=List of 3
>>> #..$ : chr [1:2] "13%" "21%"
>>> .#.$ : chr [1:10] "TWF2H101" "TWF2H102" "TWF2H103" "TWF2H104" ...
>>> #..$ : chr [1:3] "EW.INCU" "EW.17.5" "EMW"
>>>
>>> res<-lapply(lapply(seq_len(dim(a)[3]),function(i) t.test(a[dimnames(a)[[1]][1],,i],a[dimnames(a)[[1]][2],,i])),function(x) data.frame(mean=x$estimate,p.value=x$p.value))
>>> res1<-do.call(rbind,res)
>>> row.names(res1)[grep("mean of x",row.names(res1))]<-gsub("(.*\\.).*$","\\113%",row.names(res1)[grep("mean of x",row.names(res1))])
>>> row.names(res1)[grep("mean of y",row.names(res1))]<-gsub("(.*\\.).*$","\\121%",row.names(res1)[grep("mean of y",row.names(res1))])
>>> res1
>>> # mean p.value
>>> #EW.INCU.13% 22.3 0.2754842
>>> #EW.INCU.21% 29.3 0.2754842
>>> #EW.17.5.13% 20.5 0.4705772
>>> #EW.17.5.21% 16.0 0.4705772
>>> #EMW.13% 23.9 0.9638679
>>> #EMW.21% 24.2 0.9638679
>>> A.K.
>>>
>>>
>>>
>>>
>>> ----- Original Message -----
>>> From: Yao He <yao.h.1988 at gmail.com>
>>> To: arun <smartpink111 at yahoo.com>
>>> Cc: R help <r-help at r-project.org>
>>> Sent: Sunday, January 6, 2013 11:21 PM
>>> Subject: Re: [R] how to aggregate T-test result in an elegant way?
>>>
>>> Thank you，it is really helpful everytime.
>>>
>>> I didn't provide any example data because I thought it is just a
>>> question of how to report t.test() result in R.
>>> However,as you say,it is better to show more details for finding an elegant way
>>>
>>> In fact I generate a 3-dimension array like that:
>>> str(a)
>>> num [1:2, 1:245, 1:3] 47.5 NA 48.9 NA 47.5 ...
>>> - attr(*, "dimnames")=List of 3
>>> ..$ : chr [1:2] "13%" "21%"
>>> ..$ : chr [1:245] "TWF2H101" "TWF2H105" "TWF2H106" "TWF2H110" ...
>>> ..$ : chr [1:3] "EW.INCU" "EW.17.5" "EMW"
>>>
>>> I want to do two sample mean t-test between 13% and 21% for each
>>> variable "EW.INCU" "EW.17.5" "EMW".
>>>
>>> So I try these codes:
>>> variable<-dimnames(a)[[3]]
>>> O2<-dimnames(a)[[1]]
>>> for (i in variable) {
>>> print(i)
>>> print(O2[1])
>>> print(O2[2])
>>> print(t.test(a[O2[1],,i],a[O2[2],,i],na.rm=T))
>>> }
>>>
>>> I don't think it is an elegant way and I am inexperience to report raw result.
>>> Could you give me more help?
>>>
>>> Yao He
>>>
>>> 2013/1/7 arun <smartpink111 at yahoo.com>:
>>>> Hi,
>>>> You didn't provide any example data. So, I am not sure whether this helps.
>>>>
>>>> set.seed(15)
>>>> dat1<-data.frame(A=sample(10:20,5,replace=TRUE),B=sample(18:28,5,replace=TRUE),C=sample(25:35,5,replace=TRUE),D=sample(20:30,5,replace=TRUE))
>>>> res<-lapply(lapply(seq_len(ncol(dat2)),function(i) t.test(dat2[,i],dat1[,1],paired=TRUE)),function(x) data.frame(meanDiff=x$estimate,p.value=x$p.value))# paired
>>>> names(res)<-paste("A",LETTERS[2:4],sep="")
>>>> res<- do.call(rbind,res)
>>>> res
>>>> # meanDiff p.value
>>>> #AB 9.4 0.021389577
>>>> #AC 15.0 0.002570261
>>>> #AD 10.6 0.003971604
>>>>
>>>>
>>>> #or
>>>> res1<-lapply(lapply(seq_len(ncol(dat2)),function(i) t.test(dat2[,i],dat1[,1],paired=FALSE)),function(x) data.frame(mean=x$estimate,p.value=x$p.value))
>>>> names(res1)<-paste("A",LETTERS[2:4],sep="")
>>>> res1<-do.call(rbind,res1)
>>>> row.names(res1)[grep("mean of y",row.names(res1))]<-gsub("(.*\\.).*","\\1A",row.names(res1)[grep("mean of y",row.names(res1))])
>>>> row.names(res1)[grep("mean of x",row.names(res1))]<-gsub("(\\w)(\\w)(\\.).*","\\1\\2\\3\\2",row.names(res1)[grep("mean of x",row.names(res1))])
>>>> res1
>>>> # mean p.value
>>>> #AB.B 25.2 1.299192e-03
>>>> #AB.A 15.8 1.299192e-03
>>>> #AC.C 30.8 5.145519e-05
>>>> #AC.A 15.8 5.145519e-05
>>>> #AD.D 26.4 1.381339e-03
>>>> #AD.A 15.8 1.381339e-03
>>>>
>>>>
>>>> A.K.
>>>>
>>>>
>>>>
>>>> ----- Original Message -----
>>>> From: Yao He <yao.h.1988 at gmail.com>
>>>> To: r-help at r-project.org
>>>> Cc:
>>>> Sent: Sunday, January 6, 2013 10:20 PM
>>>> Subject: [R] how to aggregate T-test result in an elegant way?
>>>>
>>>> Dear all:
>>>>
>>>> Plan 1:
>>>> I want to do serval t-test means for different variables in a loop ,
>>>> so I want to add all results to an object then dump() them to an
>>>> text. But I don't know how to append T-test result to the object?
>>>>
>>>> I have already plot the barplot and I want to know an elegant way to
>>>> report raw result.
>>>> Can anybody give me some pieces of advice?
>>>>
>>>> Yao He
>>>> ―――――――――――――――――――――――――
>>>> Master candidate in 2rd year
>>>> Department of Animal genetics & breeding
>>>> Room 436,College of Animial Science&Technology,
>>>> China Agriculture University,Beijing,100193
>>>> E-mail: yao.h.1988 at gmail.com
>>>> ――――――――――――――――――――――――――
>>>>
>>>> ______________________________________________
>>>> R-help at r-project.org 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.
>>>>
>>>
>>>
>>>
>>> --
>>> ―――――――――――――――――――――――――
>>> Master candidate in 2rd year
>>> Department of Animal genetics & breeding
>>> Room 436,College of Animial Science&Technology,
>>> China Agriculture University,Beijing,100193
>>> E-mail: yao.h.1988 at gmail.com
>>> ――――――――――――――――――――――――――
>>>
>>
>>
>>
>> --
>> ―――――――――――――――――――――――――
>> Master candidate in 2rd year
>> Department of Animal genetics & breeding
>> Room 436,College of Animial Science&Technology,
>> China Agriculture University,Beijing,100193
>> E-mail: yao.h.1988 at gmail.com
>> ――――――――――――――――――――――――――
>>
>
>
>
> --
> ―――――――――――――――――――――――――
> Master candidate in 2rd year
> Department of Animal genetics & breeding
> Room 436,College of Animial Science&Technology,
> China Agriculture University,Beijing,100193
> E-mail: yao.h.1988 at gmail.com
> ――――――――――――――――――――――――――
>
--
―――――――――――――――――――――――――
Master candidate in 2rd year
Department of Animal genetics & breeding
Room 436,College of Animial Science&Technology,
China Agriculture University,Beijing,100193
E-mail: yao.h.1988 at gmail.com
――――――――――――――――――――――――――
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