[R] R package to analyze time course microarray data

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]] __ R-help@r-project.org mailing list ht

Re: [R] How to join the two tables based on one overlapped column

Hi Dan, Please ignore my previous question. I figured it out by specifying all.x=FALSE. Have a great day! Allen On Wed, Oct 8, 2008 at 8:28 PM, ss <[EMAIL PROTECTED]> wrote: > Hi Dan, > > Thanks a lot for this! It works but I have some minor issues. > Let's take

Re: [R] How to join the two tables based on one overlapped column

t; SEARCH_KEY1, PROBE_ID1, and PROBE_ID2 > > That is, you have to put SEARCH_KEY1 and SEARCH_KEY2 in quotes, which I > forgot in my previous email. > > Cheers, > Daniel > > > - > cuncta stricte discussurus > - > > >

Re: [R] How to join the two tables based on one overlapped column

- > cuncta stricte discussurus > - > > -Ursprüngliche Nachricht- > Von: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] Im > Auftrag von ss > Gesendet: Wednesday, October 08, 2008 11:33 AM > An: R help > Betreff: [R] How to join the

[R] How to join the two tables based on one overlapped column

Dear list, I need some clues on this. I have two excel files and I basically want to map one to the other one. Can you give me some hints how to do it? The first excel file, named as "Susan_probe.xls", there are two columns, "PROBE_ID1" and "SEARCH_KEY1" PROBE_ID1 SEARCH_KEY1 ILMN_30212 ILMN

[R] How to draw dot plots for 2 vectors seperately

Hi all, I want to draw dot plots for 2 rows in a matrix separately but want to have them close to each other. For example, I have a matrix a: > dim(a) [1] 319 2 and then transpose it to matrix b > b<-t(a) > dim(b) [1] 2 319 So I want to draw dot plots for these two rows separately but wan

[R] How to take the average of multiple rows

Dear all, I have a matrix, called newdata1, > dim(newdata1) [1] 3417683 It looks like: EntrezIDName S1 S2 S3S4 S5. 1 4076 CAPRIN1 0.1 0.2 0.3... 2 139170WDR40B 0.4 0.5 0.6... 35505PPP1R2P1 0.3 0.3 0.7

Re: [R] how to select out some columns using cbind()

Thank you very much, Jim! Have a good evening! Allen On Sat, Jun 14, 2008 at 7:35 PM, jim holtman <[EMAIL PROTECTED]> wrote: > newdata1 <- data1[, seq(from=2, to=ncol(data1), by=7)] > > On Sat, Jun 14, 2008 at 7:27 PM, ss <[EMAIL PROTECTED]> wrote: > > Hello! I hav

[R] how to select out some columns using cbind()

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

Re: [R] Problem with rowMeans()

x27;numeric'. I can recover the 2nd column, which is gene symbol later so I cannot worry about it for now. I just don't want you to invest your precious time on this. Thanks much, Allen On Thu, Jun 12, 2008 at 8:01 PM, ss <[EMAIL PROTECTED]> wrote: > Thanks, Erik. I will t

Re: [R] Problem with rowMeans()

is not numeric but 'factor' instead. Can I convert this column to numeric? Allen On Thu, Jun 12, 2008 at 7:48 PM, Erik Iverson <[EMAIL PROTECTED]> wrote: > > > ss wrote: > >> It is: >> >> > data <- >> read.table('E-TABM-1-processed-data-

Re: [R] Problem with rowMeans()

0586213CDNA73-1.60.16 2 A_23_P76435 15E1.2 0.180.59 3 A_24_P402115 15E1.21.63 -0.62 4 A_32_P227764 15E1.2 -0.76 -0.42 Thanks, Allen On Thu, Jun 12, 2008 at 7:34 PM, Erik Iverson <

Re: [R] Problem with rowMeans()

[EMAIL PROTECTED]> wrote: > ss wrote: > > Thank you very much, Wacek! It works very well. > > But there is a minor problem. I did the following: > > > > >data <- > > read.table('E-TABM-1-processed-data-1342561271_log2_with_symbols.txt', > > +row

Re: [R] Problem with rowMeans()

apply(data[,3:85], 2, class) == "numeric") [1] FALSE > What else should I do? I appreciate! Allen On Thu, Jun 12, 2008 at 4:55 PM, Erik Iverson <[EMAIL PROTECTED]> wrote: > Hello - > > ss wrote: > >> Hi all, >> >> I have a matrix called 'd

[R] Problem with rowMeans()

Hi all, I have a matrix called 'data', which looks like: > data[1:4,1:4] Probe_ID Gene_Symbol M1601 M1602 1 A_23_P10586213CDNA73-1.60.16 2 A_23_P76435 15E1.20.180.59 3 A_24_P402115 15E1.21.63

[R] How to plot a matrix

Hi list, If I have a matrix, > a<-read.table("a.txt",header=TRUE,row.names=1) > dim(a) [1] 4 3 > a x y z a1 1 6 3 a2 2 6 3 a3 2 3 8 a4 5 3 4 > Can you suggest how to produce a plot like the one attached here? Basically, I want to plot each sample (each column) using the dots one by one and al

[R] How to identify overlapped items from two list and plot them?

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]] _

[R] A question about *read.table()*

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_

[R] How to count the overlapped in two vectors

Dear list, If I have two vector, t1 and t2, of different lengths. Is there an easy way to count the number of the overlapped in two vectors and show the result in the graph? Thanks much, Alex [[alternative HTML version deleted]] __ R-help@r-

Re: [R] Help on read in a txt file

Try the following to see how many columns are in each line: > > x <- count.fields("A.txt", sep="\t") > which(x != 592) # print out the lines that are not correct > > You might also try: > > read.table("a.txt", sep="\t", fill=TRUE) > &g

[R] Help on read in a txt file

Dear list, Hello! I had a problem of reading in a txt file and need your help. The txt file, called A, comprises of 592 columns and 34179 rows. I need to note that for some cells of A , A[i,j], are blank. I used read.table() and got the warning message: > A<-read.table(file="A.txt",sep="\t") War

Re: [R] How to match some patterns in a matrix

matrix if it has a non-null dim > attribute (it also is a vector). > > 2. ?match or ?"%in%" tells you what to do. > > x2[x2[["name"]] %in% y,] > > is what you want. > > > > > -Original Message- > From: [EMAIL PROTECTED] [mailto:[E

[R] How to match some patterns in a matrix

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 qw22ebdbdbbbd7 4 deffrdffnnshfd3 and a vector called

[R] Describing discriminant function

hello, I have two 2-d normal multivariate distributions mapped out on a scatter plot. I now need a line that equates the two discriminant functions, ie. g1(x) = g2(x). This should be a quadratic. How can I solve this in R? Thanks -- View this message in context: http://www.nabble.com/Describing

[R] Extracting data from Eigen function

Hi I need to extract the data returned by Eigen to plot the eigenvectors. However, when I try and eigv = eigen(covariance); it returns an object with the matrices containing eigenvalues and vectors.. how can I extract the eigenvector matrix from this?? When I try mat = eig["vectors"] it returns a