similar to: how to threshold a matrix

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 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

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

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 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

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 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

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, 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

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,

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

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

Tried the following with R --vanilla on the Rv2.4.0 release (see details at the end). I think the script and its comments speaks for itself, but the outcome is certainly not wanted. for (n in 58950:58970) { cat("n=", n, "\n", sep=""); # Clean up first rm(names, x, y); gc(); # Create a named vector of length n # Try with format "%5d" and it

Hello! I need to switch from htb2 to htb3, because of speed issues (for me, htb2 is unable to handle more then 100mbit duplex with ~550 classes), kernel profiling shows htb_dequeue_prio at 1st place with 3x isolation. So, I''ve moved from 2.4.19 to 2.4.25 kernel (hi-pac for classification/marking and htb3 for queueing), and traffic rate drop from 100 to 20mbit. What can be wrong? The

I'm new to Dovecot but I've been able to get it up and running on a test basis without too much difficulty. I'm running dovecot-stable-20050508 with maildir, under Linux (an old Gentoo setup that's been stable for about 2,5 years). Mail client is Thunderbird. However, in the course of experimentally copying the accumulated household email (95000 emails from the last 10 years)

Hi All, Yesterday I began experimenting with using LDA to do delivery. To begin with I'm using a .forward file entry for myself so as to avoid affecting other users. When "deliver" is passed an item to deliver, the following is logged: > deliver(allen): Sep 18 19:28:52 Info: Namespace: type=private, > prefix=INBOX., sep=., inbox=yes, hidden=no, list=yes, subscriptions=yes

Hi Dave, I built successfully an xvm 3.3 system. However, I found virt-manager and virt-install don''t work. I attached the error messages of both as below. xm tool seems to work. I can run OpenSolaris200811 LiveCD and install it onto file based disk. The error messages of virt-manager: ====start of error message==== Unable to open connection to hypervisor URI ''xen'':

From: Allen Hubbe <allen.hubbe at amd.com> Consume the parameter to device_features when parsing command line options. Otherwise the parameter may be used again as an option name. # vdpa dev add ... device_features 0xdeadbeef mac 00:11:22:33:44:55 Unknown option "0xdeadbeef" Fixes: a4442ce58ebb ("vdpa: allow provisioning device features") Signed-off-by: Allen Hubbe

From: Allen Hubbe <allen.hubbe at amd.com> Consume the parameter to device_features when parsing command line options. Otherwise the parameter may be used again as an option name. # vdpa dev add ... device_features 0xdeadbeef mac 00:11:22:33:44:55 Unknown option "0xdeadbeef" Fixes: a4442ce58ebb ("vdpa: allow provisioning device features") Signed-off-by: Allen Hubbe