[R] Converting CSV file to numeric and calculate ttest
PIKAL Petr
petr.pikal at precheza.cz
Fri Sep 4 12:39:39 CEST 2015
Hi
Well, you want us to help you but you do not provide any relevant information
This is a result of first line of your code on my computer
> FCPval <- read.csv("C:/Users/shawin/Desktop/RProgramms/RAdipose/FCPval.csv")
Error in file(file, "rt") : cannot open the connection
In addition: Warning message:
In file(file, "rt") :
cannot open file 'C:/Users/shawin/Desktop/RProgramms/RAdipose/FCPval.csv': No such file or directory
So nobody knows what is FCPval. If you read it correctly it shall be data frame, from your previous post I presume it is numeric.
> Fc2<-(FCPVal$Fc>=2 | FCPval<=-2); this will just come out , true false
not extracting the Fc ,
you does not **extract** anything, you did not ask for extraction.
> FCP<-as.matrix(sapply(FCPval,as.numeric))
> A=as.data.frame(FCP)
Above lines are difficult to grasp. If csv file was numeric why do you want to transfer it to numeric. You shall ***read*** it as numeric at first instance. If the file is not numeric what do you expect as.numeric will do to it. It just put numeric values where they are not appropriate.
Here is an example
> lev
animals animalYears ind
1 bird 1 2
2 cat 1 2
3 dog 1 2
> as.matrix(sapply(lev,as.numeric))
animals animalYears ind
[1,] 1 1 2
[2,] 2 1 2
[3,] 3 1 2
>
I will not go deep into source of your this error, it is probably due to properties of your object A
> Fc2<-(A$Fc>=1.3| A$Fc<=-1.3) & A$p=0.05; // has error when i combine
> condition
>
> Error in (Fc2 <- (A$Fc >= 1.3 | A$Fc <= -1.3) & A$p) = 0.05 :
> could not find function "<-<-"
>
Here is how you shall do a selection, based on inbuilt iris data set
data(iris)
> dim(iris)
[1] 150 5 # so iris has 150 rows
sel <- (iris$Sepal.Width>4 | iris$Sepal.Width<3) & iris$Petal.Width==1.3
iris[sel,]
Sepal.Length Sepal.Width Petal.Length Petal.Width Species
54 5.5 2.3 4.0 1.3 versicolor
56 5.7 2.8 4.5 1.3 versicolor
59 6.6 2.9 4.6 1.3 versicolor
65 5.6 2.9 3.6 1.3 versicolor
72 6.1 2.8 4.0 1.3 versicolor
75 6.4 2.9 4.3 1.3 versicolor
88 6.3 2.3 4.4 1.3 versicolor
90 5.5 2.5 4.0 1.3 versicolor
95 5.6 2.7 4.2 1.3 versicolor
97 5.7 2.9 4.2 1.3 versicolor
98 6.2 2.9 4.3 1.3 versicolor
100 5.7 2.8 4.1 1.3 versicolor
Only 12 are extracted so with proper data everything works. If you want better answer please provide at least result of
str(yourdata)
but preferably the data itself e.g. by
dput(head(FCPval, 20))
Petr
PS. And read R intro as it seems you do not understand R basics.
> -----Original Message-----
> From: R-help [mailto:r-help-bounces at r-project.org] On Behalf Of shawin
> Sent: Thursday, September 03, 2015 1:55 PM
> To: r-help at r-project.org
> Subject: Re: [R] Converting CSV file to numeric and calculate ttest
>
> Dear Petr,
>
> This code does not work ?
> For selection values you can use e.g. [
> data(iris)
> sel<-iris$Sepal.Width>4
> iris[sel,] or iris[sel, c(1,3,5)]
>
>
> the data is csv file which is :
> FCPval <-
> read.csv("C:/Users/shawin/Desktop/RProgramms/RAdipose/FCPval.csv")
>
> ;
>
> Fc2<-(FCPVal$Fc>=2 | FCPval<=-2); this will just come out , true false
> not extracting the Fc ,
> #######################################################################
> ##############################
> FCP<-as.matrix(sapply(FCPval,as.numeric))
> A=as.data.frame(FCP)
> Fc2<-(A$Fc>=1.3| A$Fc<=-1.3) & A$p=0.05; // has error when i combine
> condition
>
> Error in (Fc2 <- (A$Fc >= 1.3 | A$Fc <= -1.3) & A$p) = 0.05 :
> could not find function "<-<-"
>
> write.csv(Fc2,"Fc2.csv",row.names =FALSE )
>
> please need help
>
>
> On Thu, Sep 3, 2015 at 8:56 AM, Shawin Karim <shawinkarim at gmail.com>
> wrote:
>
> > Oh sorry F<2 & F<-2 , i need to extract the row value according to
> > the last two column F,P and using condition ,
> >
> > I attached an test file to see the data
> >
> > On Thu, Sep 3, 2015 at 8:43 AM, PIKAL Petr [via R] <
> > ml-node+s789695n4711787h96 at n4.nabble.com> wrote:
> >
> >> Hi
> >>
> >> what is F?
> >>
> >> F>2 & F<2
> >> this is FALSE for all values of F
> >>
> >> What value you want to extract? All rows corresponding to condition
> >> or just values from specific column.
> >>
> >> For selection values you can use e.g. [
> >> data(iris)
> >> sel<-iris$Sepal.Width>4
> >> iris[sel,] or iris[sel, c(1,3,5)]
> >>
> >> Cheers
> >> Petr
> >>
> >> From: Shawin Karim [mailto:[hidden email]
> >> <http:///user/SendEmail.jtp?type=node&node=4711787&i=0>]
> >> Sent: Thursday, September 03, 2015 9:17 AM
> >> To: PIKAL Petr
> >> Subject: Re: [R] Converting CSV file to numeric and calculate ttest
> >>
> >> I solve it , thanks but i have an issue please :
> >>
> >>
> >> have a csv file and i would like to extract the value of it with
> >> specific range fof the last column for example; F>2 & F<2 & P=1, and
> >> then write the result to csv file.
> >>
> >> the data is :
> >> x1
> >>
> >> x2
> >>
> >> x3
> >>
> >> x4
> >>
> >> x5
> >>
> >> x6
> >>
> >> 9.488404
> >>
> >> 9.470895
> >>
> >> 9.282434
> >>
> >> 9.366707
> >>
> >> 9.955383
> >>
> >> 9.640816
> >>
> >> 8.63063
> >>
> >> 8.558311
> >>
> >> 8.788391
> >>
> >> 8.576231
> >>
> >> 8.671588
> >>
> >> 8.84298
> >>
> >> 9.354749
> >>
> >> 9.367669
> >>
> >> 9.259953
> >>
> >> 9.421538
> >>
> >> 9.554635
> >>
> >> 9.603745
> >>
> >> 9.944864
> >>
> >> 9.950428
> >>
> >> 10.19102
> >>
> >> 10.07351
> >>
> >> 10.0327
> >>
> >> 10.13079
> >>
> >>
> >> Fc
> >>
> >> p
> >>
> >> 1.037883
> >>
> >> 0.320095
> >>
> >> 1.057708
> >>
> >> 0.060132
> >>
> >> 1.065191
> >>
> >> 0.111192
> >>
> >>
> >>
> >>
> >> I tried the code bellow but , it does not work?
> >>
> >> FCPval <-
> >> read.csv("C:/Users/shawin/Desktop/RProgramms/RAdipose/FCPval.csv")
> >>
> >> c=as.data.frame(FCPval)
> >>
> >> for (i in 1:rowN){if (C$F[i] >= 2 && C$F[i]<=-2&& C$p[i]<=3){
> >>
> >> dfrmPFC=data.frame(Fc=FC,p=p)}
> >> }
> >>
> >> the error is :
> >>
> >> Error in C$FC : object of type 'closure' is not subsettable.
> >>
> >> can i extract the value according to the condition
> >>
> >> On Thu, Sep 3, 2015 at 8:14 AM, PIKAL Petr <[hidden email]
> >>
> <http:///user/SendEmail.jtp?type=node&node=4711787&i=1><mailto:[hidde
> >> n email] <http:///user/SendEmail.jtp?type=node&node=4711787&i=2>>>
> >> wrote:
> >> Hi
> >>
> >> p value of what? How do you know that it should be 0.3?
> >>
> >> Your HTML post is mangled and almost unreadable.
> >>
> >> Your code is not reproducible, we do not have AT1.csv
> >>
> >> AT1 shall be numeric so your reading process is wrong and following
> >> conversion to numeric shall be umnnecessary if you read your data
> properly.
> >>
> >> Cheers
> >> Petr
> >>
> >> > -----Original Message-----
> >> > From: R-help [mailto:[hidden email]
> >>
> <http:///user/SendEmail.jtp?type=node&node=4711787&i=3><mailto:[hidde
> >> n email] <http:///user/SendEmail.jtp?type=node&node=4711787&i=4>>]
> On
> >> Behalf Of shawin
> >> > Sent: Wednesday, September 02, 2015 9:08 PM
> >> > To: [hidden email]
> >>
> <http:///user/SendEmail.jtp?type=node&node=4711787&i=5><mailto:[hidde
> >> n email] <http:///user/SendEmail.jtp?type=node&node=4711787&i=6>>
> >> > Subject: Re: [R] Converting CSV file to numeric and calculate
> ttest
> >> >
> >> > p value should be 0.3
> >> >
> >> > On Wed, Sep 2, 2015 at 8:07 PM, Navien [via R] < [hidden email]
> >> > <http:///user/SendEmail.jtp?type=node&node=4711787&i=7>
> >> <mailto:ml-node%[hidden email]
> >> <http:///user/SendEmail.jtp?type=node&node=4711787&i=8>>> wrote:
> >> >
> >> > > I have a csv file i convert it to numeric value , then i apply
> >> > > t-test , but t-test result is not correct: please could you
> guide
> >> > > me. the
> >> > data :
> >> > > ID x1 x2 x3 x4 x5 x6 x7 x8 x9 x10 x11 x12 x13 x14 x15 1367452_at
> >> > > 9.488404158 9.470895414 9.282433728 9.366707445 9.955383045
> >> > > 9.640816474 9.606262272 9.329651027 9.434541611 9.473922432
> >> > > 9.311412966
> >> > > 9.3154885 9.434977488 9.470895414 9.764258059 1367453_at
> >> > > 8.630629966
> >> > > 8.55831075 8.788391003 8.576231135 8.671587906
> >> > > 8.842979993 8.861958856 8.58330436 8.603596508 8.570129609
> >> > > 8.59798922
> >> > > 8.572686772 8.679751791 8.663950953 8.432875347 1367454_at
> >> > 9.354748885
> >> > > 9.367668838 9.259952558 9.421538213 9.554635162
> >> > > 9.603744578 9.452197983 9.284228877 9.404607878 9.317737979
> >> > > 9.343115301
> >> > > 9.310644266 9.27227486 9.360337823 9.44706281 1367455_at
> >> > > 9.944863964
> >> > > 9.950427516 10.19101759 10.07350804 10.03269879
> >> > > 10.1307908 10.03487287 9.74609383 9.886379007 9.775472567
> >> > > 10.036596
> >> > > 9.544738458 9.699611598 9.911962567 9.625804277
> >> > > AT1 <-
> >> > > read.csv("C:/Users/shawin/Desktop/RProgramms/RAdipose/AT1.csv",
> >> > > stringsAsFactors=TRUE)
> >> > >
> >> > >
> >> > > str(AT1)
> >> > > matAT = data.frame(AT1[,-1])
> >> > > str(matAT)
> >> > > write.csv(matAT,"matAT.csv",row.names=FALSE)
> >> > > #convert the csv file to numeric
> >> > > matAT<-as.matrix(sapply(matAT,as.numeric))
> >> > > str(matAT)
> >> > > group<-factor(rep(c("Ob","Ln"),times=c(7,8)))
> >> > > t.test(matAT[1,]~group)
> >> > >
> >> > >
> >> > >
> >> > >
> >> > >
> >> > >
> >> > >
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