similar to: read.table & readLines behaviour?

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

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 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 was wondering if there's a way in R to open a web browser (such as Internet Explorer, or Firefox or whatever). I'm doing some analyses that have associated urls, and it would be nice to have the ability to directly open the relevant page from within R. I was looking at the help for 'url' and I can see I can probably access the information I need and display it in my

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, after reading about it in the forum, I tried the Tinn-R editor (in WinXP) running R 2.5.0... nice one! However, I am trying to change the syntax-colouring from the default to my own preferences... and I can do that, but my options don't appear to be saved and get lost when I close Tinn-R. I've searched help menus, and google... and I can't find how to make sure my

Hi everyone, is there a way/package in R that would allow me to select a group of points from a scatterplot by drawing a circle around them or some such? I can use 'identify' to pick individual points, but that gets tedious if one has more than 10-20 spots. I can easily select spots within a rectangle defined by picking points using identify... but a simple rectangle sometimes will

Hello list, I use R for microarray analysis. One procedure I use takes a large matrix, and loops through it looking for specific rows, does an operation with them, and outputs a result (single row) as a row of another matrix. The loop goes on about 25000 times. When I run the loop directly from the R console itself, it takes about 3 minutes in my computer. I'm ok with that. Now,

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

I'm trying something that I thought would be pretty simple, but it's proving quite frustrating... I want to display, for instance, the correlation coefficient "rho" in a graph. I can do something like: text(x, y, paste("rho =", cor)) where cor would be my previously calculated correlation coefficient, and x and y the coordinates. Obviously that displays

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

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, 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,

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

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

Hi All, I've hit a problem using nls. I think it may be a restriction in the applicability of nls and I may have found a fix, but I've been wrong before. This example is simplified to the essentials. My real application is much more complicated. Take a function of matrix 'x' with additional arguments: matrix 'aMat' whose values are _not_ to be determined by nls vector

Dear list, is there a way to open a .zip folder so that one can extract and modify files inside and then save teh .zip folder again? thanks! Jose -- Dr. Jose I. de las Heras Email: J.delasHeras at ed.ac.uk The Wellcome Trust Centre for Cell Biology Phone: +44 (0)131 6507095 Institute for Cell & Molecular Biology Fax: +44 (0)131 6507360 Swann Building,

***********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

Hi everyone, I hope there's a simple way to achieve what I want, but I haven't found the way. I do microarray analysis using R and a number of packages as well as some functions created my myself. When I save the workspace, it saves all the data structures, that's great... But when I click (I'm on Windows XP, if it matters) on teh resulting .RData file, I have to reload

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