similar to: merged files

Hi, i have two files (file1.txt and file2.txt) which i would like to merge, based on certain criteria, i.e. it combines data based on matching geneID and exons. i have used the merge option, but it does not give me the desired outcome. merged.txt shows the result i would like. *File1. txt* ** AffyProbe ProbeType Flag GeneSymbol GeneID Exons Chrom Strand Affytart AffyEnd 1

Hi, I have the following function: > kurtosis <-function(x) (mean((x-mean(x))^4))/(sd(x)^4) #x is a vector and data > print(mydata) V1 V2 V3 V4 V5 1 1007_s_at DDR1 2865.1 2901.3 1978.3 2 1053_at RFC2 103.6 81.6 108.0 3

Hi, I have the following data frame: > print(mydatframe) __DATAFRAME__ V1 V2 V3 1 1007_s_at DDR1 discoidin domain receptor tyrosine kinase 1 2 1053_at RFC2 replication factor C (activator 1) 2, 40kDa 3 117_at HSPA6 heat shock 70kDa protein 6 (HSP70B') __END__ Is there a way to create a hash with V2 as Key and V3 as its value? - Gundala Viswanath Jakarta - Indonesia

Hi, I have the following data file to be parsed and captured as a data frame: __DATA__ #GDS_ID GENE_NAME GENE_DESCRIPTION GENE_FUNCTION 1007_s_at | DDR1 | discoidin domain receptor tyrosine kinase 1 | protein-coding 1053_at | RFC2 | replication factor C (activator 1) 2, 40kDa | protein-coding 117_at | HSPA6 | heat shock 70kDa protein 6 (HSP70B') | protein-coding __END__ In particular it is

R-users, I have the following piece of code which I am trying to run on a dataframe (aga2) with about a half million records.  While the code works, it is extremely slow.  I've read some of the help archives indicating that I should allocate space to the p1 and ags1 vectors, which I have done, but this doesn't seem to improve speed much.  Would anyone be able to provide me with advice on

Hi all, Suppose I have a vector like this: [1] "STAT1" "STAT1" "STAT1" "STAT1" "GAPDH" "GAPDH" "GAPDH" "ACTB" "ACTB" [10] "ACTB" "DDR1" "RFC2" "HSPA6" "PAX8" "GUCA1A" "UBE1L" "THRA" "PTPN21" [19]

hi all i started recently using R and i found myself stuck when i try to analyze microarray data. i use the "affy" package to obtain the intensities of the probes, i have two CTRs and two treated. HG.U133A.Experiment1.CEL HG.U133A.Experiment2.CEL HG.U133A_Control1.CEL HG.U133A_Control2.CEL 1007_s_at 2156.23115 467.75615 364.60615 362.11865

hell all: I have a vector as follows: > head(res) 1007_s_at.value 1053_at.value 117_at.value 121_at.value 1255_g_at.value 0.225801033 0.009747404 0.709517954 0.008825740 0.496859178 1294_at.value 0.005091231 after I convert the res into a data frame I got the following: resx<- data.frame(res) > head(resx) res

Hello all! I am currently trying to sort a data frame in a particular way, but I am having some difficulties with this. Specifically I want to sort the below dataset in such a way that there is only one line per ProteinID and if there are multiple GeneID or GeneName entries for a single proteinID, that they be concatenated with a comma separating them. The way I have done it earlier worked fine

Is there any function/way to merge/unite the following data GENEID col1 col2 col3 col4 G234064 1 0 0 0 G234064 1 0 0 0 G234064 1 0 0 0 G234064 0 1

Dear all, I want to use string split to parse column names, however, I am having some errors that I don't understand. I see a problem when I try to rbind the output from strsplit. please let me know if I'm missing something obvious, thanks, alison here are my commands: >strsplit<-strsplit(as.character(Rumino_Reps_agreeWalign$geneid),"\\.") >

Dear List, I am trying to modify the xlab and ylab for a current figure that was plotted by a package, I searched through the low level plotting command and they do not seem to contain how to do this (the only way is to use xlab, ylab as arguments in "plot" command, which I can not do since the plot is plotted using some other package, not by my own script). Is there any command for

I'm trying to find a clever way to re-map data from a database query into a data.frame. Querying a database often returns a table (data.frame) like this: GeneID MethodID Value 6 1 123 6 2 456 6 3 987 7 1 234 7 3 432 8 2 190 8 3 34 8 1 864 Note that GeneID=7 doesn't have a value for MethodID=2. Note that GeneID=8 doesn't have the

Hi, With the following codes, I attempt to convert the data.frame into a matrix. However I notice that data.matrix function doesn't seem to work. __ BEGIN__ dat <- read.table("mydata", comment.char = "!" , na.strings = "null"); # Select n-genes by random sample # n = 1 nosamp <- 1 geneid <- sequence(nrow(dat)) geneid.samp <- sample(geneid,nosamp)

Dear mailing list, I have a C function that gives me a wrong result when I run it under Windows 7. This is the code under Linux (RHEL5): > library(phenoTest) > data(epheno) > sign <- sample(featureNames(epheno))[1:20] > score <- getFc(epheno)[,1] > head(score) 1007_s_at 1053_at 117_at 121_at 1255_g_at 1294_at -1.183019 1.113544 1.186186 -1.034779 -1.044456

Hi Everyone, I am very new to R. When i run the code yesterday, it was working fine. I was able to find gene annotation. somehow, today, when i try to run it again, it is giving me errors message that i don't understand. It says that it cannot open file. what file is it looking for? ###################################################### ##make sure to install and load annotationtool in R

Dear All: I have a question on using coxph for multiple genes: I have written code to loop through all 22283 genes in the Hgu-133A and apply coxph on survival data. However, I don't know how to work with the result for each gene: survtest<-coxph(Surv(pcc.primary.stg.3.cox[,'fup_interval'],pcc.primary.stg.

Hi all, I originally posted this to the bioconductor group, but maybe it's better suited to the r-help... I'm using som() to partition samples of gene expression data into clusters. The point is to classify control vs. experimental cases (sample clustering). The original matrix was 22283 x 8. The 8 samples have 4 controls and 4 experimentals. I transposed the matrix so that its dim

Hi everyone, I've been using nut 2.0.3 for more than a year on a Unitek iZi UPS 525 (which is a rebadged Mustek). Everything worked fine and last week, when pressed by RENEL :-) I ran a battery test which showed the system to have 17min of back-up power (yes, still haven't figured out how to use upssched...) The system used for testing was an old PIII/500MHz/512KB cache, 256MB RAM (3 x

I am trying to use a new (to me) package (samr) and even when I try to run a very simple example, I get this "cannot open the connection" error. The reason I am writing to r-help rather than to the authors of samr is I think this may be a more general R problem rather than a samr-specific problem. Perhaps something with my installation and write access to some particular place ? I am