search for: gene2

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    TF2    0.2    Gene1    TF3    0.2 Gene2    TF1    1.4 Gene2    TF2    0.0 Gene2    TF3    2.8 Gene3    TF1    0.3 Gene3    TF2    0.6 Gene3    TF3    1.7 Gene6000...TF200...etc The matrix is ~60...

...tch rows from a data frame which matches to first 2 columns of another data frame. Here is the example what I am trying to do: > ptable=read.table(file="All.txt",header=T,sep="\t") > ptable=as.matrix(ptable) > dim(ptable) [1] 9275 6 > head(ptable) Gene1 Gene2 PCC PCC3 PCC23 PCC123 [1,] "3813_f_at" "3884_f_at" "0.9956842" "0.9955455" "0.9956513" "0.9956171" [2,] "3884_f_at" "3813_f_at" "0.9956842" "0.9955455" "0.9956513&quot...

...tion to unix data server. Our problem today is : Only one smbd daemon has been started when user comes from W2k server. Behind this unique unix process, there is a management of about 70 - 100 connections.... This is a result part of "smbstatus" : rimuno rimuno genra 5319 gene2 (193.50.63.0) Tue Oct 22 15:00:29 2002 winto winto genra 5319 gene2 (193.50.63.0) Tue Oct 22 15:01:03 2002 thoyon thoyon sepes 5319 gene2 (193.50.63.0) Tue Oct 22 15:00:25 2002 Prod_Contr kurbel genra 5319 gene2 (193.50.63.0) Tue Oct 22 15:00:22 2002 Temporaire bouc...

...a is as below: ------------------------------------------------------------------------------------------------ Sample.ID Gene tissue.type batch(lab) expression.level id1 gene1 liver batch1 0.67 id1 gene2 liver batch1 0.89 id2 gene1 kidney batch1 0.52 id2 gene2 kidney batch1 0.45 . . id10 gene1 brain batch4...

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 value gene1 ----------------------------- gene1 1 10 10 gene1 2 20 20 gene1 3 50 100 gene2 1 20 10 gene2...

...ratio_exp123.RData") #calculation correlation and p-values of genes using rcorr function y_cor_p123=rcorr(t(ratio_exp123),type="pearson") save(y_cor_p123,file="y_cor_p123.RData") diag(y_cor_p123$r)=0 #Selecting gene pairs with pcc value greater than 0.8 gene1=matrix(0,1,1) gene2=matrix(0,1,1) pcc=matrix(0,1,1) for(i in 1:nrow(y_cor_p123$r)) { for(j in 1:nrow(y_cor_p123$r)) { if(y_cor_p123$r[i,j]>0.8) { gene1=rbind(gene1,rownames(y_cor_p123$r[i,j,drop=F])) gene2=rbind(gene2,colnames(y_cor_p123$r[i,j,drop=F])) pcc=rbind(pcc,y_cor_p123$r[i,j]) } } } y_gp123=cbind(gene1,gen...

hi, folks: i need to transpose the following data: gene tissue patient1 patient2 patient3..... --------------------------------------------- gene1 breast 10 100 1 gene2 breast 20 200 4 gene3 breast 30 50 5 gene4 breast 40 400 9 ................................ to the following format: patientID gene1 gene2 gene3 gene4............ ------------------------------------------- 1...

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 1200 gene3 75 998 gene3 71 910 I have found one post with the same problem (...

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 everyone, I have a data frame (tt), see below (I only show 2 genes, actually I have a lot): group gene1 gene2 Control 28.9776 9.9355 Control 28.9499 10.0997 Control 29.5468 14.2995 Control 29.5246 13.9561 Test1 29.1864 9.7718 Test1 29.2048 10.0388 Test1 34.9563 11.9509 Test1 34.9464 11.8909 Test2 36.9566 14.5316 Test2 37.1309 14.5188 Test2 36.1017 29.5468 Test2 36.0883 29.5246 I'd like to cal...

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]]

Dear all, Once again I need your help ; I fond a way to do what I want but I am sure there is a better way.. maybe you can help me. I have a matrix, for example mat.tot : > mat.tot ID Desc M1 M2 1 1 gene1 0.5 0.2 2 2 gene2 -0.4 -0.1 3 3 gene3 1.0 1.2 4 4 gene1 0.6 0.3 5 5 gene2 -0.3 0.0 and I want to merge line 1 with line 4, and line 2 with line 5 because this is the same gene. I can do that with the "merge" function but I need to make 2 "virtual" matrices, like this : > ind<-duplicat...

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 11 gene2 7.0 222 8 gene3 0.2 3 8 gene4 3.0 10 10 gene5 0.1 5...

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 chr1 30 40 11 + I just wondering is there an efficient way to find *overlapped, upstream and downstream genes for each gene in the granges* For example, assuming al...

Dear Sir/Madam, I found your email address and your correspondence with R-users. I hope you could help me with this question about the function "ur.ers" in the package of "urca". It is an improved unit root test (Elliott et al. 1996 Econometrica). Do you know how to extract the value of the test statistic from the output? The only thing I can get is the print-out of all

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

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 chr1 30 40 11 + I just wondering is there an efficient way to find overlapped, upstream and downstream genes for each gene in the granges For example, assuming all_...

...- matrix(c(0.96, 0.07, 0.97, 0.98, 0.50, 0.28, 0.29, 0.77, 0.08, 0.96, 0.51, 0.51, 0.14, 0.19, 0.41, 0.51), ncol=4, byrow=TRUE) colnames(test) <- c("Exp1","Exp2","Exp3","Exp4") rownames(test) <- c("Gene1","Gene2","Gene3", "Gene4") test <- as.table(test) mat = data.matrix(test) heatmap.2(mat, dendrogram="row", Rowv=TRUE, Colv=FALSE, distfun = function(x) dist(x,method = ''maximum''), hclustfun = function(x) hclust(x,method = ''centroid...

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

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 the "second principal axis" of this analysis? Aoife [[alternative HTML version deleted]]