similar to: help with reshape is needed again!

hi, everyone: i have a question on the reshape function. i have the following dataset : gene tissue patient1 patient2 patient3............. _________________________________________________ gene1 breast 10 20 50 gene2 breast 20 40 60 gene3 breast 100 200 300 which i hope to convert to the following format: gene patientID

Hey guys, can anyone help? i have a sample table: >table <- structure(c(4, 7, 0.2, 3, .1, 7, 222, 3, 10, 5, 11, 8, 8, 10, 7), .Dim = c(5L, 3L), .Dimnames = list(c("gene1", "gene2", "gene3", "gene4", "gene5"), c("codon1", "codon2", "codon3"))) >table codon1 codon2 codon3 gene1 4.0 7

I have 2 files containing data analysed by 2 different methods. I would like to find out which genes appear in both analyses. Can someone show me how to do this? _________________________________________________________________ [[trailing spam removed]] [[alternative HTML version deleted]]

I do have a bunch of genes ( nearly ~50000) from the whole genome, which read in genomic ranges A range(gene) can be seem as an observation has three columns chromosome, start and end, like that seqnames start end width strand gene1 chr1 1 5 5 + gene2 chr1 10 15 6 + gene3 chr1 12 17 6 + gene4 chr1 20 25 6 + gene5

Hello everyone, I am running a mixed effects model where I have two fixed factors, one with 2 levels and one with 4, and their interaction. Let's say these are my factors and their levels: FirstFactor: 1, 2 SecondFactor: A, B, C, D For the interaction, I am interested in the four two-way comparisons, not the two four-way comparisons. In other words, I want to test whether 1A is

Hey guys, if i do a correspondance analysis, e.g.: table <- structure(c(4, 7, 0.2, 3, .1, 7, 222, 3, 10, 5, 11, 8, 8, 10, 7), .Dim = c(5L, 3L), .Dimnames = list(c("gene1", "gene2", "gene3", "gene4", "gene5"), c("codon1", "codon2", "codon3"))) Library(ca) plot(ca(table)) is there a way that i can see

Hi, I've looked through the posts but couldn't find a solution to this. I'd be really grateful if someone could help, I'd like to convert a data file of mutual information that is formatted as a matrix:             TF1    TF2    TF3    TF200... Gene1    0.0    0.2    0.2 Gene2    1.4    0.0    2.8 Gene3    0.3    0.6    1.7 Gene6000.... To a list: Gene1    TF1    0.0 Gene1   

Hi all, I have been struggling with this problem for a few days. I have a data table like this: gene rpkm1 diff1 rpkm2 diff2 gene1 23 50 13 120 gene2 111 220 827 1200 gene3 75 998 71 910 And I want to re-format it so that, for each gene, I have a 2x2 contingency table, such as: gene rpkm diff gene1 23 50 gene1 13 120 gene2 111 220 gene2 827

I am making some changes to the permax library (so that it will accept NA's). This function performs a permutation analysis to identify discriminating attributes distinguishing two groups of observations. It takes the form (at its most simplistic): permax(data, ig1) where ig1 is one group of interest. The other group (if not specified) is assumed to be the remaining observations, namely,

Hello all! I have the following problem with the %in% command: 1) I have a data frame that consists of functions (rows) and genes (columns). The whole has been loaded with the "read.delim" command because of gene-duplications between the different rows. 2) Now, there is another data frame that contains all the genes (only the genes and without duplicates) from all the functions of

Hey guys, Can anyone help? I did a correspondance analysis and made a plot. I also have a specific list of nodes that i want to find in my plot and want to either color the nodes that appear in my list differently, or put some kind of border around that group of nodes... Would anyone know how to do this? Also, would this post be more relevant here or in the bioconductor forum? -- View this

I have data set up like the following: control1 <- sample(1:75, 3947398, replace=TRUE) control2 <- sample(1:75, 28793, replace=TRUE) control3 <- sample(1:100, 392733, replace=TRUE) control4 <- sample(1:75, 858383, replace=TRUE) patient1 <- sample(1:100, 28048, replace=TRUE) patient2 <- sample(1:50, 80400, replace=TRUE) patient3 <- sample(1:100, 48239, replace=TRUE) control

Hi, this might be basic but can't get it to work and it is hampering my R usage: #the loop is checking variance of rows, and cutting out rows with var>numVec[i] #I define outMat as object names I want to output to (does this make sense? how else #can I define sequential numbered output?) #numVec is numbers I use in the loop head(Counts) AN1 AN2 AN3 AN4 var GENE1

I do have a bunch of genes ( nearly ~50000) from the whole genome, which read in genomic ranges A range(gene) can be seem as an observation has three columns chromosome, start and end, like that seqnames start end width strand gene1 chr1 1 5 5 + gene2 chr1 10 15 6 + gene3 chr1 12 17 6 + gene4 chr1 20 25 6 + gene5

Hello: I am a novice R user, but I have been working my way through the manuals / tutorials, ... I have R / Deducer up and running, and know the basics. I want to analyze a microarray (gene expression) dataset. I need to input the data into R as a multidimensional (multi-way) array, something on the order of 15,000 x 3 x 8 x 2 [genes x replicates x time points x treatments] I've

Hello All, I have posted to this list before regarding the same issue so I apologize for the multiple e-mails. I am still struggling with this issue so I thought I'd give it another try. This time I have included reproducible code and a subset of the data I am analyzing. I am running an ANOVA with three factors: GROUP (5 levels), FEATURE (2 levels), and PATIENT (2 levels), where

Dear list, I have been struggling with this for some time now, and for the last hour I have been struggling to make a working example for the list. I hope someone out there have some experience with plotting longitudinal data that they will share. My data is some patient data with three different time stamps. First the patients are identified at different times (first time stamp). Second, they

hi I want to compare two list by its names and get the values of that list. can anybody let me know the syntax of comparing the list by their names using a for loop c.genes<- list() for(i in 1:100) c.genes[[1]]<- geneset(which(geneset == tobecampared[i])) } here geneset is a list and also tobecampared is a list Thank you Ramya -- View this message in context:

Dear All, I have two factors: GROUP and PATIENT, where PATIENT is nested within GROUP. >levels(example$GROUP) [1] "0" "1" "2" "3" "4" > levels(example$PATIENT) [1] "1" "2" "3" There are three observations at each combination of these factors. However, there are no observations for PATIENT = 3 and GROUP

Hello, I'm pretty new to R. Basically, how do I speed up the for loop below. Or better yet, get rid of the for loop all together. objective: plot two data sets column against column by index. These data sets have alot NA's. Some columns are all NA's. I need the plots to overlay. I don't like the plots in matplot(). Needs to be much faster than the code below... #simple sample