search for: affysnp

Dear list, I need to read in a big table with 487 columns and 238,305 rows (row names and column names are supplied). Is there a code to read in the table in a fast way? I tried the read.table() but it seems that it takes forever :( Thanks a lot! Best, Allen

Hello list, I have a data frame M like: BAC chr pos s1 s2 RP11-80G24 1 77465510 -1 0 RP11-198H14 1 78696291 -1 0 RP11-267M21 1 79681704 -1 0 RP11-89A19 1 80950808 -1 0 RP11-6B16 1 82255496 -1 0 RP11-210E16 1 228801510 0 -1 RP11-155C15 1 230957584 0 -1 RP11-210F8 1

Hi list, Is there a way to read in a txt file with some blanks? The ideal way could be to replace blanks with NAs. Thanks a lot! Allen [[alternative HTML version deleted]]

Hi list, My data set is comprised of 47 columns and about 700 rows. Most of the values would be around 2, while some will go beyond in either direction, higher or lower. Is there a way to specify the parameter of col or others if necessary to have the range of representing colors be 0----8, and make dark for 2, red for higher than 2 and green for lower than 2. Is there a way to do this? Thanks a

Dear list, I am using heatmap.2(x) to draw a heatmap. Ideally, I want to the matrix x clustered only by columns and keep the original order of rows unchanged. Is there a way to do that in heatmap.2()? Thanks a lot! Any suggestions will be appreciated! Best, Allen [[alternative HTML version deleted]]

Dear list, I have a matrix M (2500 rows and 9 columns). It looks like 2.2 0.1 2.6 3.6 ...... 0.4 1.9 2.7 4.2...... 1.8 2.5 4.3 2.2....... ..................... If I want to do: (1) if M[i,j]>=0.3, M[i,j]=1 (2) if M[i,j]<=-0.3, M[i,j]=-1 (3) Otherwise, M[i,j]=0 Is there a way to ceil and floor the data? Thanks a lot! Allen [[alternative HTML

Hello! I have a matrix: > dim(data1) [1] 34176 581 of 34176 rows and 581 columns, I want to make a new matrix data2 by taking the 2nd column, 9th column, 16th column.... the column number is in the order of: 2 9 (2+7) 16 (9+7) 23 (16+7) ... the new matrix data2 should include 83 columns, is there an easy way to do that using cbind() function? Thanks a lot! Allen [[alternative HTML

Dear list, I have a data frame (238304 rows and 6 columns). I want the data frame sorted by two columns in ascending order. I am showing the first 5 rows of the data frame > clones.info[1:5,1:6] USER_CLONE_ID CHROMOSOME Expr1002 KB_POSITION Allele_A WELL_ID 1 SNP_A-1855402 17 41419603 41419603 C rs17572851 2 SNP_A-4249904 17 41420045 41420045 A rs17572893 3 SNP_A-2174835 18 41407760

> Dear list, > I have a data frame like: > > > log2.ratios[1:3,1:4] > ID a1 a2 a3 > 1 GS1-232B23 -0.0207500 0.17553833 0.21939333 > 2 RP11-82D16 -0.1896667 0.02645167 -0.03112333 > 3 RP11-62M23 -0.1761700 0.08214500 -0.04877000 > 4 RP11-62M23 0.2761700 -0.15214500 -0.05877000 > the 3rd and

Hello list, I read in a txt file using <B<-read.table(file="data.snp",header=TRUE,row.names=NULL) by specifying the row.names=NULL so that the rows are numbered. Below is an example after how the table looks like using <B[1:10,1:3] SNP Chromosome PhysicalPosition 1 SNP_A-1909444 1 7924293 2 SNP_A-2237149 1 8173763

...istinfo/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: 75 Date: Wed, 21 Nov 2007 21:43:07 -0500 From: "affy snp" <affysnp at gmail.com> Subject: [R] Heatmap problem To: r-help at r-project.org Message-ID: <5032046e0711211843y2eebdb9eia0ab282a63a3a8ff at mail.gmail.com> Content-Type: text/plain Hi friends, I used heatmap(as.matrix(y2),col=rainbow(256),scale = "column") to generate the heatmap....

Hi friends, I used heatmap(as.matrix(y2),col=rainbow(256),scale = "column") to generate the heatmap. But it did not show the code that which color correspond the value. Is there any parameter for this in heatmap()? Thanks a lot! Allen [[alternative HTML version deleted]]

Dear list, I have a data frame like: > log2.ratios[1:3,1:4] Clone a1 a2 a3 1 GS1-232B23 -0.0207500 0.17553833 0.21939333 2 RP11-82D16 -0.1896667 0.02645167 -0.03112333 3 RP11-62M23 -0.1761700 0.08214500 -0.04877000 how to make it to look like: > log2.ratios[1:3,1:4] a1 a2

Dear list, I am wondering if there are any parameters in heatmap.2 to be able to adjust the size of row labels. Or the size of the plot can be made smaller. The plot I got is big and cannot see the full row labels completely. And what is the maximum of rows which could allow row labels visible in the plot? Last time, I tried a matrix of 2900 rows, but apparently the row labels are too dense to

Dear all, I have a data frame called x2, which looks like: > dim(x2) [1] 2237 2 > x2[1:4,1:2] name id 1 STye hggd3 2 STy2 bffbd2 3 qw22e bdbdbbbd7 4 deffrdff nnshfd3 and a vector called y, which looks like: > dim(y) [1] 135 1 > y[1:3,1] [1] ABCDE BDH5 DESRP1 y is a

Hello! Just want to get some suggestions on which R package is good for analyzing time course microarray data. Thank you so much for your input! Sincerely, Allen [[alternative HTML version deleted]]

Hi list, I have a question about using *read.table()* to read in a txt file. Basically, it consists of 16346 rows, 6 columns (no header). The code I used is: exprSet <- read.table('process_all4_GSA2.txt', row.names = 1,header =FALSE) and I got an error message: > exprSet <- read.table('process_all4_GSA2.txt', row.names = 1,header =FALSE) Error in

Dear list, Hello! I have a question about how to print a label in the plot. I am using the following code: <pdf("mel4_chr3_11cancer_cghFLasso.pdf", height=6, width=5);plot(Disease.FL, index=i, type="Single",main="Plot of Labels");dev.off(); But "Plot of Labels" has not been printed. Any suggestions? Thanks a lot! Allen

Hi list, I have a question on how to identify the overlapped items from two vectors: >x<-c(0,1,2) >y<-c(1,2,2,3) and plot the number of the overlapped as well as non-overlapped in a diagram? Thanks much, Allen [[alternative HTML version deleted]]

Dear list, I have a question about using plot(). I tried the code: <pdf("mel_chr_all_13cancer_cghFLasso_all.pdf", height=6, width=11);plot( Disease.FL, index=1:4, type="All");dev.off(); and it went through well which outputed 4 plots for 4 samples in one page. But if I increase the numbers of plots(samples) which I want, saying to 11,