[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

[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 each one.

[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

[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 table in excel sample_drug sample_control

[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) When

Re: [R] Newbie: Incorrect number of dimensions

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 #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

[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 = NA)

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 is the orginal data: short

[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

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: Hello, Thanks everyone

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: sorry...in step 4-i need the R code to output

[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],

[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: Measuring distance between clusters.

. 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: Measuring distance between clusters. Hi, I had 1 genes, and I

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 and elsewhere. I re-install bioconductor source, update

[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

[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 to R. How

[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 =

[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

[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])