[R] Calculating Distance Metrics using Euclidean

I am trying to calculate the distance metrics, but i keep getting this error. I am very new to R. Am i doing something wrong. > dim(data.sub) [1] 1 140 > dist(data.sub, method = "euclidean", diag = FALSE, upper = FALSE, p = 2) Error: cannot allocate vector of size 781250 Kb In addit

[R] Calculating the distance samples using distance metics method

***reading in data** data<-read.table("microarray.txt",header=T, sep="\t") head(data) dim(data) attach(data) ***creating matrix and calculating variance across probesets x<-1:2 y<-2:141 data.matrix<-data.matrix(data[,y]) variableprobe<-apply(data.matri

[R] Calculating the Distance

***creating matrix and calculating variance across probesets x<-1:2 y<-2:141 data.matrix<-data.matrix(data[,y]) variableprobe<-apply(data.matrix[x,],1,var) hist(variableprobe) **filter out low variance* data.sub = data.matrix[order(variableprobe,d

[R] Newbie: Measuring distance between clusters.

Hi, I had 1 genes, and I clustered them using K-means clustering in R. kc<-kmeans(data.sub,7) kc n cluster sum of squares by cluster: [1] 60631.76 135886.19 159049.71 101783.27 90040.72 183335.60 158867.81 Available components: [1] "cluster" "centers" "withinss" "size" I am very new t

[R] exprs function download

Hi, I am supposed to use exprs as a function. Where can i download exprs function? I tried searching at bioconductor and seach engine but no luck. Is it located in one of the library in R? thanks. C -- View this message in context: http://www.nabble.com/exprs-function-download-tp15654560p15654

Re: [R] Newbie: Measuring distance between clusters.

fine distances between clusters, though. > There are many possibilities. > > -Original Message- > From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] > On Behalf Of Keizer_71 > Sent: Saturday, 23 February 2008 7:40 PM > To: r-help@r-project.org > Subject: [R] Newbie: Meas

Re: [R] Newbie: Where is lmFit function?

thank you. Chuck Cleland wrote: > > On 2/24/2008 4:02 PM, Keizer_71 wrote: >> Hi Everyone, >> >> I am trying to use lmFit function; however, i cannot find it function >> anywhere. >> >> I have been trying to find the function in Bioconductor a

[R] Newbie: Where is lmFit function?

Hi Everyone, I am trying to use lmFit function; however, i cannot find it function anywhere. I have been trying to find the function in Bioconductor and elsewhere. I re-install bioconductor source, update package and update R as well. no luck Is there a command in R where i can just type, and i

[R] Newbie: Incorrect number of dimensions

> dim(data.sub) [1] 1 140 #extracting all differentially express genes## library(multtest) two_side<- (1-pt(abs(data.sub),50))*2 diff<- mt.rawp2adjp(two_side) all_differ<-diff[[1]][37211:1,] all_differ #list of differentially expressed genes## > probe.names<- +

Re: [R] Newbie: Incorrect number of dimensions

roducible code. > > What does str(all_differ) say? That will tell you the structure of > the object that you are trying to work with. > > On Sat, Mar 1, 2008 at 3:35 AM, Keizer_71 <[EMAIL PROTECTED]> wrote: >> >> > dim(data.sub) >> [1] 1 140 >

[R] Newbie:Export Data into Excel from R

Hi, All i want is to export my list into c: drive and save it as csv file and manually import into Excel. I have the read the article but i am having issues http://pbil.univ-lyon1.fr/library/base/html/write.table.html > excel<-write.table(probe_gene, file = "c:\foo.csv", sep = ",", col.names =

Re: [R] Variance Calculation in R

sorry...in step 4-i need the R code to output in this format when i export to excel. ProbeID Variance 1 224588_at 21.58257457 thanks Keizer_71 wrote: > > Hello, > > Thanks everyone for helping me with the previous queries. > > step 1: Here i

[R] Variance Calculation in R

Hello, Thanks everyone for helping me with the previous queries. step 1: Here is the orginal data: short sample ProbeID Sample_1_D Sample_1_CSample_2_D Sample_2_C 1 224588_at 2.425509867 11.34031409 11.46868531 11.75741478 step 2: i calculate the v

Re: [R] Variance Calculation in R

Hi Henrique, It is definitely better, but it doesn't show me the ProbeID which identify the probes name Here was the result when i export to excel with your code. "Variance" 1 2.425509867 21.6216446425273 any suggestions? thanks, Kei Keizer_71 wrote: > &g

Re: [R] Variance Calculation in R

unfortunately, it is not showing probeID Henrique Dallazuanna wrote: > > Try this: > > write.table(cbind(data.matrix[1], Variance = apply(data.matrix[,-1], > 1, var)),file='file.xls') > > > On 02/03/2008, Keizer_71 <[EMAIL PROTECTED]> wrote: >

[R] R data Export to Excel

Here is my R Code x<-1:2 y<-2:141 data.matrix<-data.matrix(data[,y])#create data.matrix variableprobe<-apply(data.matrix[x,],1,var) variableprobe #output variance across probesets hist(variableprobe) #displaying histogram of variableprobe write.table(cbind(data[1], Variance=apply(data[,y],1,

[R] Calculating the t-test for each row

Hi Everyone, I need some simple help. Here are my codes ##will give me 1 probesets data.sub = data.matrix[order(variableprobe,decreasing=TRUE),][1:1,] dim(data.sub) data_output<-write.table(data.sub, file = "c://data_output.csv", sep = ",", col.names = NA)

[R] Export csv data

Hi Everyone, Thanks for all the help with the previous queries. Here is what i want to do. i have 2 probesets-->calculate all the variance accross all the probesets-->filter out probesets that are low so now i ended up with only 1. The 1 is fine but when i export to excel, it is miss

[R] paired or one-sample t-Test

Hi Guys, I am having a real hard time trying to figure out for microarry. Here is my code One-Sample t-Test dim(data.sub) [1] 1 140 ##there are 1 probesets and 140 columns hist(data.sub) ## Histogram. Identify if the probesets are normal distributed q<-rnorm(1) ##generate 1

[R] paired t-Test in R

Keizer_71 wrote: > > Hi Guys, > > I am having a real hard time trying to figure out for microarry. > > Here is my code > > One-Sample t-Test > > dim(data.sub) > [1] 1 140 ##there are 1 probesets and 140 columns > > Example of the t

[R] Excel export into R

Hello, I have this in excel Control 543_BU 123_AT 432_CU I want to be able to import to R so that it will read like this c<-c("543_BU","123_AT","432_CU") output: [1] "543_BU" "123_AT" "432_CU" This is just a short version. I have about 20 rows and i need a simpler way instead of typing

Re: [R] Excel export into R

Hi Richie, I apologize. I thought i deleted this thread since it is resolved by using scan() function. thank you again, Kei Richard Cotton wrote: > >> I have this in excel >> >> Control >> 543_BU >> 123_AT >> 432_CU >> >> >> I want to be able to import to R so that it will read like this >

[R] Statistical Questions: finding differentially expressed genes

Hi Everyone, I am trying to find a way to do this in excel to tell me which genes are the most differentially expressed. Sorry, i couldn't find excel forum section in nabble. However, if it is in R it is fine. This is a microarray data, and it has been normalized. According to Dov Stekel in Micro

[R] expression matrix

Hello, I am to run this R script but i keep getting this error. > expr<-exprs(golubMerge) Warning message: The exprSet class is deprecated, use ExpressionSet instead I tried to find information on the website but no luck. (exprSet...etc) thank you. -- View this message in context: http://ww

[R] expression matrix

Hello, I am to run this R script but i keep getting this error. > expr<-exprs(golubMerge) Warning message: The exprSet class is deprecated, use ExpressionSet instead I tried to find information on the website but no luck. (exprSet...etc) thank you. -- View this message in context: http://ww

[R] R error: Not able to launch R 2.6.2

Hi Everyone, I am having trouble using R. I am not sure what happen but when i start R, i am getting error message "Fatal Error: Unable to restore saved data in .RData. -I restarted my pc but still same error -I reinstall R but still same error -deleted the R folder and have a fresh re-install

[R] p-adjust using Benjamn and Hochberg

Hello, I am trying to use the p.adjust function for multiple testing. here is what i have 9997201674_s_at 0.327547396 9998221013_s_at 0.834211067 221685_s_at 0.185099475 I import them from excel have have the gene symbol as well as the pva