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...#39;,'cumulMetric') ? ? ??? #return whole list ??? return(listMetric)# dataframe } Cheers i --- On Sat, 18/12/10, cstrato <cstrato at aon.at> wrote: > From: cstrato <cstrato at aon.at> > Subject: Re: [BioC] problem with function > To: "Iain Gallagher" <iaingallagher at btopenworld.com> > Cc: "bioconductor" <bioconductor at stat.math.ethz.ch> > Date: Saturday, 18 December, 2010, 14:40 > You need to do: > > cumulMetric <- function(deMirPresGenes, deMirs){ > ??? fc <- deMirs > ??? fcVector <- as.numeric(with (fc...

Hello list I have been given some Excel sheets with data laid like this: Col1 Col2 A 3 2 3 B 4 5 4 C 1 4 3 I was hoping to import this into R as a csv and then get the mean and SD for each letter in column 1. Could someone give me some guidance on best to approach this? Thanks Iain

Hello List I'm trying to calculate the median period (in months) of a set of time intervals (between two interventions). I have been playing with the lubridate package to create the intervals but I can't think of the right approach to get the median timeperiod. Toy code: library(lubridate) test <- c('08-04-22', '08-07-28', '09-03-02', '09-03-03',

Hello list. I am hoping for some help with a relatively simple problem. I have a data frame arranged as below. I want to be able to count the occurrence of each gene (eg let-7e) by Experiment. In other words how many times does a given gene crop up in the dataframe. I tried table but couldn't work out how to get the output I want. I have also considered rearranging this data into a list (by

Hello I have a Linux machine (Ubuntu 8.04 hardy, Gcc version 4.2.4 (i486-linux-gnu) currently running R 2.6.2. I'd like to upgrade to 2.10. First Question): What is the appropriate way to remove the old version of R? Part 2. After downloading r-base_2.10.0.orig.tar.gz and opening the archive. I ran the ./configure routine. It failed claiming that it could not find the F77 compiler. My

Hi. I have two vectors of gene expression for each of several days. I want to plot both vectors on the same plot for a visual representation of up versus down regulation. I've tried using add=T but that doesn't work. eg >plot(Day, gene1) >plot(Day, gene2, add=T) Any help would be appreciated. Iain

Hello List I have a list question. I'm doing some data wrangling for a colleague and I have nested list in the following format: structure(list(MU10 = structure(c(0.80527905920989, 0.4350488707836, 0.455195366623, 0.565174432205497, 0.208180556861924), .Names = c("MU.16", "MU.19", "MU.21", "mean", "sd")), MU11 =

Hello list I have a problem with a dataset (see toy example below) where I am trying to find the difference between two (or more numbers) and discard those observations which fall outside a set interval. An example and further explanation: values ind 1 2655 7A5 2 3028 7A5 3 689 ABBA-1 4 1336 ABBA-1 5 1560 ABBA-1 6 2820 ABLIM1 7 3339 ABLIM1 8

Hi List I have a dataframe (~1,200,000 rows deep) and I'd like to conditionally reorder groups of rows in this dataframe. I would like to reorder any rows where the Chr.Strand column contains a '-' but reorder within subsets delineated by the Probe.Set.Name column. # toy example #### library(plyr) negStrandGene <- data.frame(Probe.Set.Name =

Hello everyone. How do I get R to ask users for data to be entered? Specifically I want to ask for a z score to be entered (the user would look this up in a table) and then use the entered data to compute a Dunn's post-hoc test (post kruskal.test). I've tried the "ask" function but it's not recognised - maybe I don't have to appropriate libary installed. A pointer

Hi List I have data in the following form: Gene    TFBS NUDC     PPARA(1) HNF4(20) HNF4(96) AHRARNT(104) CACBINDINGPROTEIN(149) T3R(167) HLF(191) RPA2     STAT4(57) HEB(251) TAF12     PAX3(53) YY1(92) BRCA(99) GLI(101) EIF3I     NERF(10) P300(10) TRAPPC3     HIC1(3) PAX5(17) PAX5(110) NRF1(119) HIC1(122) TRAPPC3     EGR(26) ZNF219(27) SP3(32) EGR(32) NFKAPPAB65(89) NFKAPPAB(89) RFX(121)

Dear List I am trying to draw a heatmap using ggplot2. In this heatmap I have faceted my data by 'infection' of which I have four. These four infections break down into two types and I would like to reorder the 'infection' column of my data to reflect this. Toy example below: library(ggplot2) # test data for ggplot reordering genes <- (rep (c(rep('a',4),

...://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. ------------------------------ Message: 18 Date: Wed, 29 Jun 2011 16:24:55 +0100 (BST) From: Iain Gallagher <iaingallagher at btopenworld.com> To: r-help at r-project.org Subject: [R] median time period Message-ID: <1309361095.68973.YahooMailClassic at web86705.mail.ird.yahoo.com> Content-Type: text/plain; charset=utf-8 Hello List I'm trying to calculate the median period (in months) of a set of time...

Hi. I would like to add a horizontal line to each column of data on a stripchart (vertical=T) to indicate the mean(rather like the package Prism does - for those that have used this) for each dataset. I presume the best way to do this would be with "lines" but after much trying / playing about I can't figure it out. Can anyone help? Thanks

Hello list. Is it possible to use par(srt=45) to rotate text by 45 degrees along the x-axis of a plot. Using: <code> x_names<-c("C57 Nv", "C57 Vacc", "129 Nv", "129 Vacc", "IFNgR Nv", "IFNgR Vacc") par(srt=45) mtext(font=2, x_names, side=1, line=1, at=l, cex=1.2) par(srt=0) </code> doesn't seem to work in R 2.2.0

Hi I'm trying to install the RBGL package. However I am getting the following error; can anybody shed some light on what I'm missing? /usr/lib/gcc/i486-linux-gnu/4.1.2/../../../../include/c++/4.1.2/cstdlib:135: error: ‘::system’ has not been declared Thanks. Iain > sessionInfo() R version 2.7.2 (2008-08-25) i486-pc-linux-gnu locale:

Hi Everyone. I am rather new to R and I've been trying to implement a function to carry out the above test. For a couple of days now I've been stuck on how to generate average rank differences. Say I have a vector of average ranks: averank<- c(2,5,9,12) I would like to subtract averank[1] from averank[2], averank[1] and averank[2] from averank[3] and averank[1], averank[2] and

Hi List I have a series of zip archives each containing several files. One of these files is called goCats.txt and I would like to read it into R from the archive. It's a simple tab delimited text file. pathToZip <- '/home/iain/Documents/Work/Results/bovineMacRNAData/deAnalysis/afInfection/commonNorm/twoHrs/af2hrs.zip' z <- unz(pathToZip, 'goCats.txt', 'r') zT

Hello list. I have a vector of values: eg > head(diff_mirs_list) [1] "hsa-miR-26b" "hsa-miR-26b" "hsa-miR-23a" "hsa-miR-27b" "hsa-miR-29a" [6] "hsa-miR-29b" and I would like to conditionally replace each value in this vector with a number defined in a dataframe: > fc ???????????? Probe ave.fc 1?????? hsa-let-7a?? 1.28 2?????

Hi list. I have a numerical dataset 22,000 rows deep and 43 columns wide. I would like to remove those rows which contain only values less than 100 (ie if any value in the row is greater than 100 the row stays in the dataset). I am unsure how to test each individual value across the rows and then identify the rows which meet my criteria. Can anyone help? Thank you. Iain [[alternative HTML