similar to: correlatation matrix

Hi there, I recently switched to Mac and I wonder if there is any way to get the R console to autocomplete names of list objects or slots of objects. The command line version allows to type e.g. list$ and two times the tab button and then comes up with the names of the list objects. Same for slots of e.g. Eset objects like eset. Unfortunately this does not work in the Mac R console. Is there a

Hi there is it possible that pdfs generated using the pdf() function with default settings leads to loss of information? I was plotting copy number changes from Agilent 180k data in form of rectangles (rect()) while each rectangle represents one region of copy number change. When plotting into a pdf I noticed that some very small rectangles do not appear (even after extensive zooming) in the pdf

Hi I try parallelising some code using the snow package and the following lines: cl <- makeSOCKcluster(8) pfunc <- function (x) (if(x <= (-th)) 1 else 0) ###correlation coefficient clusterExport(cl,c("pfunc","th")) cor.c.f <- parApply(cl,tms,c(1,2),FUN=pfunc) The parApply results in the error message: > cor.c.f <- parApply(cl,tms,c(1,2),FUN=pfunc) Error

Dear R-users, I'm using lattice package and function xyplot for the first time so you will excuse me for my inexperience. I'm facing quite a simple problem but I'm having troubles on how to solve it, I've read tons of old mails in the archives and looked at some slides from?Deepayan Sarkar but still can not get the point. This is the context. I've got data on 9 microRNAs, each

Hi everyone, I am trying to find a way to filter a table; If I am given for example the following table: > head(intra) chr miRNA start end strand ACC hsa_ID region region_start region_end gene_id transcrip_id 1 chr1 miRNA 1102484 1102578 + ACC="MI0000342"; ID="hsa-mir-200b"; exon 1102484 1102578 NR_029639 NR_029639 2 chr1

Hi All, I wonder if there should be one character for quote= in read.table, i.e., > args(read.table) function (file, header = FALSE, sep = "", quote = "\"'", dec = ".", ... I have a file containing the following lines, 08248-GOTERM 3'-phosphoadenosine 5'-phosphosulfate biosynthetic process 08279-GOTERM 3'-phosphoadenosine

Dear All, I would like to ask for help on how to read different files automatically and do analysis using scripts. 1. Description of the data 1.1. there are 5 text files, each of which contains cleaned data for the same 100 SNPs. Observations (e.g., position on gnome, alelle type, ...) for SNPs are rows ordered by the SNP numbers, 1.2. there are 1 text file, containing the expression level of

Hi, After manipulate my data I have ended up with 5 different data frames with different number of observations but the same number of variables (columns) An example, if I write str(object1), I see this, data.frame': 47 obs. of 3 variables: $ ORF : Factor w/ 245 levels "YAL038W","YAL054C",..: 10 19 38 39 44 45 50 51 59 60 ... $ mRNA : num 0.891 1.148 1.202

Hi all! While I am trying to read .cel files with oligo package: afbatch=read.celfiles(list.celfiles()) I get an error: Package 'pd.mirna.1.0.2xgain' was not found in the BioConductor repository How can I overcome this? Thank you in advance

I wonder whether R provides an interface to access miRecords data. Particularly, I am looking for extracting humans miRNA and target genes sequences. All such information is stored in there in a set of structured web site pages (http://mirecords.umn.edu/miRecords) I would greatly appreciate any suggestion even about other data bases from where it is possible to get the same sort of data. I had a

Hi all, I'm having some trouble in understanding how to ste the Error() term in the aov() function when fitting a hierarchical ANOVA. I have data concerning the expression of 2 miRNAs in 3 different cell lines, with 2 different extraction methods. The data is organized as follows : Line Extraction Target Expression 1 BC54 miRNA RNU48 22.48 2 BC54 miRNA

Dear All, I have two matrices A (40 x 732) and B (40 x 1230) and would like to calculate correlation between them.  I can use: cor(A,B, method="pearson") to calculate correlation between all possible pairs. But the issue is that there is one-many specific mappings between A and B and I just need to calculate correlations for those pairs (not all). Some variables in A (proteins, say p1)

Unluckily I dela with miRNA files whose name may contain the character "*". Because of the special meaning of "*" I have to remove it. I found out how to make list.files() extract only those file names which contain a "*" Namely: # list.files(pattern="\\*") Now I have to process all files whose name does NOT contain the character "*". I cannot

For any given pre-specified gene or short list of genes, yes the Cox model works fine. Two important caveats: 1. Remeber the rule of thumb for a Cox model of 20 events per variable (not n=20). Many microarray studies will have very marginal sample size. 2. If you are looking at many genes then a completely different strategy is required. There is a large and growing literature; I like Newton

I have the following files list: > list.files() [1] "Prostate-Cancer_cvs_Dir" [2] "Prostate_Cancer-miRNAs&Genes.Pathway.xml" [3] "Prostate_Cancer_Pathways-miRNAs-GeneTargets-Dir" [4] "Prostate_Cancer_Pathways-miRNAs-GeneTargets-Dir.zip" [5] "Prostate-miRNAs.OrganTargets.txt"

Dear Sir: > I am a chinese researcher who interested in miRNA, and I want to use R to analysis my data.I have download R-2.4.0-win32.exe and install it smoothly on my > computer,but when I want to use this software, error occurs,it shows" R for > > windows GUI front-end meet some problems" and the interface closese > automatically, I don't know what happen.

Dear All, I am analyzing the miRNA data set in which I have 817 unique probes for each they have 20 features each . I have to group the similar features and take the median across them so that I have a data with no repeats to perform invariant analysis . My data looks something similar format probename sample1 sample2 sample3 A 2.3 2.4 2.5 A

Hi, I have a question about heatmap. I have a data with row as microRNA and two columns are two cell expression values for these microRNA. So, like: cell1 cell2 miRNA1 1.5 3.4 miRNA2 1.3 2.4 ................... miRNA50 5 2.1 miRNA51 7.3 0.5 I want to see some miRNA are high in cell1 and low in cell2 but others are low in cell1 and high in cell2. I

Hello, I have a seemingly simple problem that a tab-delimited file can't be read in. > annoTranscripts <- read.table("matched.txt", sep = '\t', stringsAsFactors = FALSE) Error in scan(file, what, nmax, sep, dec, quote, skip, nlines, na.strings, : line 5933 did not have 12 elements However, all lines do have 12 columns. > lines <-

Hi! I would like to select probes (affy expression set) of genes that are "cancer-related". Conventionally the decision whether a gene is cancer-related or not is made by looking up the literature. Since this is not possible for all genes on the array I wonder if there is a way of doing this automatically? Best wishes Kristian -- _____ Dr Kristian Unger Imperial College London