similar to: Calculating the distance samples using distance metics method

Here is my R Code x<-1:20000 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,var)),file='c://variance.csv') #export as a .csv file. Output in Excel all in 1

Hi Everyone, I need some simple help. Here are my codes ##########will give me 10000 probesets#################### data.sub = data.matrix[order(variableprobe,decreasing=TRUE),][1:10000,] dim(data.sub) data_output<-write.table(data.sub, file = "c://data_output.csv", sep = ",", col.names = NA) When i export to excel, it shows me this. This is just a short version. There

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_C Sample_2_D Sample_2_C 1 224588_at 2.425509867 11.34031409 11.46868531 11.75741478 step 2: i calculate the variance of the sample using this R code x<-1:20000 y<-2:141 data.matrix<-data.matrix(data[,y])#create data.matrix

Hi Everyone, Thanks for all the help with the previous queries. Here is what i want to do. i have 20000 probesets-->calculate all the variance accross all the probesets-->filter out probesets that are low so now i ended up with only 10000. The 10000 is fine but when i export to excel, it is missing the probeID. Here are my code and examples. #########calculate the variance across the

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] 10000 140 ##there are 10000 probesets and 140 columns hist(data.sub) ## Histogram. Identify if the probesets are normal distributed q<-rnorm(10000) ##generate 10000 random, normal distributed values qqplot(data.sub,q)) ##Show the plot of the probeset

Hi, I have been using 'read.table' regularly to read tab-delimited text files with data. No problem, until now. Now I have a file that appeared to have read fine, and the data inside looks correct (structure etc), except I only had 15000+ rows out of the expected 24000. Using 'readLines' instead, and breaking up the data by tabs, gives me the expected result. I do not

Hi, I am relatively new to R and Bioconductor and am trying to filter the topTable that I generated of differentially expressed genes from my normlized eset file comprised of ~ 40 HG-133A Affy microarrays . I would like to see if particular probesets are represented in this list. Alternatively I would like to generate a topTable of differentially expressed genes using only specified probesets

Hi, I have a question concerning the analysis of some affymetrix chips. I downloaded some of the data from GEO GSE11324 (see below). In doing so I'm stuck after I identified the probesets with significant changes. I have problems in assigning probeset specific gene names as well as getting the genomic coordinates. Furthermore I have no clue how to deal with the fact, that most genes have

> dim(data.sub) [1] 10000 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]][37211:10000,] all_differ #####list of differentially expressed genes########## > probe.names<- + all_differ[[2]][all_differ[[1]][,"BY"]<=0.01] Error in

Hello: I am trying to work with a couple of microarray data sets, using platform i386-pc-mingw32 arch i386 os mingw32 system i386, mingw32 status major 1 minor 8.1 year 2003 month 11 day 21 language R In the shortcut for invoking R I have set

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 it will download it for me? -- View this message in context:

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) Error in file(file, ifelse(append, "a", "w"))

Dear all, I would like to know how to subset a data.frame by rows. Example: Probesets 34884 34888 34892 1 100009676_at A A A 2 10001_at P P P 3 10002_at A A A 4 10003_at A A

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://www.nabble.com/expression-matrix-tp15912874p15912874.html Sent from the R help mailing list archive

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-tp15654560p15654560.html Sent from the R help mailing list archive at Nabble.com.

Hello, I am trying to use the p.adjust function for multiple testing. here is what i have 9997 201674_s_at 0.327547396 9998 221013_s_at 0.834211067 9999 221685_s_at 0.185099475 I import them from excel have have the gene symbol as well as the pvalue here is the issue > pa<-p.adjust(pt,method="BH") Error in p[nna] : object is not

I think that you misunderstood me. As far as I know, RMA does three things: background correction, quantile normalization, and summary from probes to probesets. I want the probe values after background correction and quantile normalization but before the summary. On Sat, Dec 26, 2009 at 12:07 PM, Benilton Carvalho <bcarvalh at jhsph.edu> wrote: > pm(data) > > b > > On Dec

Hi, I have built R (current development version) and BioConductor 1.7 with portland group compiler on a AMD Opteron. When I ran qc assessment on Affymetrix latin square data set, I got the following output, Loading required package: affy Loading required package: Biobase Loading required package: tools Welcome to Bioconductor Vignettes contain introductory material. To view,

Dear All, I'm dealing with a case, where 'manhattan' distance of each of 100 vectors is calculated from 10000 other vectors. For achieving this, following 4 scenarios are tested: 1) scenario 1: > x<-read.table("query.vec") > v<-read.table("query.vec2") > d<-matrix(nrow=nrow(v),ncol=nrow(x)) > for (i in 1:nrow(v)){ + d[i,]<-

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 200000 rows and i need a simpler way instead of typing each one. thanks -- View this message