similar to: Drosophila Genome 2.0 annaffy annotation

Hi everybody, I have a problem when trying to do the quality control with the packages simpleaffy and affyQCReport with the drosophila chip 2.0 At first I got the messeage, that the *.qcdef file is not there. I followed the instructions in tha manual and created the file like that: array drosophila2cdf alpha1 0.05 alpha2 0.065 spk bioB AFFX-r2-Ec-bioB-3_at spk bioC AFFX-r2-Ec-bioC-3_at spk bioD

Problem################################################################# I am having a problem combining a matrix and elements of a list into one data frame. Data#################################################################### The matrix is ludwig.results and dim of matrix is 213,8. The list is called symbols and its length is 213. Following is an example the structure of my matrix

Hi all, I am trying to download, decompress and read a csv file. My code: myurl <- "ftp://ftp.ncbi.nih.gov/pub/geo/DATA/supplementary/series/GSE24729/GSE24729_MitoNuclear_suppl_male_stats.csv.gz" # myfile <- "GSE24729_MitoNuclear_suppl_male_stats.csv.gz" # download.file(myurl, destfile=myfile, mode="w") # mycon <- gzcon(gzfile(myfile,

Full_Name: Colin A. Smith Version: 1.8.0 OS: Mac OS X 10.2.6 Submission from: (NULL) (216.102.90.18) Both Biobase and my package annaffy use S4 classes to define methods for "[". Both packages use the save image method of installation. (See annaffy 1.0.3 in BioC CVS.) Depending on how both packages are loaded, the Biobase definitions seem to be getting masked out: >

Full_Name: Colin A. Smith Version: 1.8.0 OS: Mac OS X 10.2.6 Submission from: (NULL) (128.102.184.81) annaffy 1.0.1 (in BioC CVS) fails to load. annaffy 1.0 (on the BioC web site) has the same problem. It looks like the load is failing because of a bug in completeSubclasses() in r-devel. It calls setIs() and doesn't specify an environment via the "where" argument. setIs()

Genome Institute of Singapore (GIS) Biostatistics Group The Genome Institute of Singapore ( http://www.gis.a-star.edu.sg <http://www.gis.a-star.edu.sg> ) is looking for statisticians who are interested in a wide range of biomedical probems. We are especially interested in hearing from senior researchers interested in leading their own group. The institute is well-funded and engaged

We are seeking a talented and driven postdoctoral fellow to join the laboratory of Jake Michaelson, PhD, assistant professor in the department of psychiatry at the University of Iowa. The Michaelson lab investigates the effect of genetic variation on the development and function of the brain, particularly in the context of neurodevelopmental conditions such as autism and language impairment. Our

Hello, I am using R to look at whole-genome gene expression data. This means about 27,000 genes, each with a vector of numbers reflecting expression at different tissues and times. I need to do an all against all co-expression calculation (basically, just calculate Pearson's r for every gene-gene pair). I try to store the result of such a thing in a 27000x27000 matrix, but r seems not to like

Hi, I have a set of genes and its chromosomal physical position in a text file. I want to view those genes in the chromosome using R package GenePlotter. Could any one please tell how to view this. Thanks in advance. Yours sincerely, S.Mahalakshmi [[alternative HTML version deleted]]

Hello, Please have a look at the code below, which I use to read in the attached file. As line 18 of the file reads "1065:>sp|Q9V3T9|ADRO_DROME NADPH:adrenodoxin oxidoreductase, mitochondrial OS=Drosophila melanogaster GN=dare PE=2 SV=1", I expect the code below to produce a 3 column data frame with most of the last column empty and line 18 to produce a data.frame row like so:

Hi, I was wondering I'm going about this in the correct way. I need to test if there are coding sequences or exons in hg19 which match a string of 100bp "D" i.e. [A,G or T]. However I'm getting a strange result. I get a hit on chr7, using the 100bp search however when I search with 60bp sequence of "D" I don't get any hits. library("BSgenome")

I am a relative newbie to survival analysis and R in general, but would like to use the coxme package to analyse some data I currently have. The data is relative to survival times of drosophila melanogaster populations to infection with pathogens, and has the variables: Time, Status, Treatment (4 treatments + 2 controls) Population Replicate ?and I'm currently using the following call

Neither biocLite nor the GUI menus can install packages on my system. Here is relevant output: > version _ platform i386-pc-mingw32 arch i386 os mingw32 system i386, mingw32 status major 2 minor 11.1 year 2010 month 05 day 31 svn rev 52157 language R version.string R version 2.11.1 (2010-05-31) > source("http://bioconductor.org/biocLite.R") BioC_mirror =

Hi, I am trying to install Bioconductor onto R version 2.7.0 for Windows. I installed R, then followed the instructions on http://www.bioconductor.org/download, which state that you should type the following: source("http://bioconductor.org/biocLite.R") biocLite() When I do that, I get the following error: Running biocinstall version 2.2.9 with R version 2.7.0 Your version of R

I have run into a problem loading a just saved R object using R-devel. I have been saving and loading this particular type of R object for a long while and never ran into this problem. I save, then immediately reload (to test save) and get "ReadItem: unnknown type 65". This error is reproducible after logout from server and restart of emacs and R. Below is my output and

I have run into a problem loading a just saved R object using R-devel. I have been saving and loading this particular type of R object for a long while and never ran into this problem. I save, then immediately reload (to test save) and get "ReadItem: unnknown type 65". This error is reproducible after logout from server and restart of emacs and R. Below is my output and

Dear all, Here is my code which am using to combine 5th column from different data sets. Here is the function to do my job genesymbol.append.file <-NULL gene.column <- NULL readGeneSymbol <- function(files,genesymbol.column=5){ for(i in fnames){ temp <- read.table(fnames,header=T,sep="\t",stringsAsFactors=F,quote="\"")

hi all, Am new to R. I am having problems installing Bioconductor package in R on fedora core 4 running on AMD64 bit machine. this is the error message I get : gcc -shared -L/usr/local/lib -o affyPLM.so avg_log.o biweight.o chipbackground.o common_types.o do_PLMrlm.o do_PLMrma.o do_PLMthreestep.o idealmismatch.o LESN.o lm.o lm_threestep.o log_avg.o matrix_functions.o

I've started to implement checks for package versions on dependencies in install.packages(). However, this is revealing a number of problems/misconceptions. (A) We do not check versions when loading namespaces, ahd the namespace registry does not contain version information. So that for example (rtracklayer) Depends: R (>= 2.7.0), Biobase, methods, RCurl Imports: XML (>=

I am unable to load a just saved R object. Get message "ReadItem: unknown type 65" I am using R-devel and the problem is reproducible after logout and restarting R. Output and sessionInfo() below. Mark > setwd("~/Genomics/Experiments.Genomic/BB01/acb.shell") > local(save(affy.object.preprocessed, file ="affy.object.preprocessed.R" )) >