similar to: paired or one-sample t-Test

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: 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, 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

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

***********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<-1:20000 y<-2:141 data.matrix<-data.matrix(data[,y]) variableprobe<-apply(data.matrix[x,],1,var) hist(variableprobe) **************filter out low

I am in need of someone's help in correlating gene expression. I'm somewhat new to R, and can't seem to find anyone local to help me with what I think is a simple problem. I need to obtain pearson and spearman correlation coefficients, and corresponding p-values for all of the genes in my dataset that correlate to one specific gene of interest. I'm working with mouse Affymetrix

Suspect that this is easier than I realize, but taking some figuring out currently. Any help would be appreciated. I have a data frame (testhm) with many rows such as: ProbeSet.ID.F ProbeSet.ID Feature.ID G.S X0030V120810.14 X0143V120110.14 X0258V111710.14 X0283V111710.14 X0430V120710.14 X0472V111610.14 X0520V111610.14 X0546V113010.14 X0578V111810.14 X0624V111810.14 2 7892501_943979

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

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 I'm running the latest R on a presumably up to date Linux server. 'Doing something silly I'm sure, but can't see why my saved PLMset objects come out all wrong. To use an example: Setting up an example PLMset (I have the same problem no matter what example I use) > library(affyPLM) > data(Dilution) # affybatch object > Dilution = updateObject(Dilution)

dear members, i would like to write a variable in a plot title (main="") but i don't know the right syntax:(...i tried a lot of different ways without success. here my example: y=30 z=33 for (i in 10:length(tissue)) { png(filename = tissues[i], width = 1024, height = 768, pointsize = 12, bg = "white") gene.graph("ENSG00000115252", rma.affy, gps=list(1:3,

I have a data matrix with genes as columns and samples as rows. I want to create all possible gene ratios.Is there an elegant and fast way to do it in R and write it to a dataframe? Thanks for any help. Som. -- View this message in context: http://r.789695.n4.nabble.com/Calculating-all-possible-ratios-tp4627405.html Sent from the R help mailing list archive at Nabble.com. [[alternative HTML

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 All, I need your help. I am analysing affymetrix data and have to select the probe-set that has median expression among all the probe-sets for same gene. This way I want to remove the redundancy by keeping the analysis to single gene entry level. I am fully aware that it is not a nice thing to do but I just have to do it. To do so, I came across 'findLargest' function of

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

Hi, What is the reason for getting two different max of a vector from two functions max() and summary()? Here is an example, > set.seed(2222) > x <- sample(x=1:100000, size=10000, replace=T) > max(x) [1] 99992 > summary(x) Min. 1st Qu. Median Mean 3rd Qu. Max. 6 24510 49950 50020 75040 99990 Which value is the correct one? I had this problem while I

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,

> 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