[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

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 the working example for instance

[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

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

them to PROBE_ID1 (i.e. replace PROBE_ID1 by the values in this column). Cheers, Daniel - cuncta stricte discussurus - -Ursprüngliche Nachricht- Von: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] Im Auftrag von ss Gesendet: Wednesday

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

discussurus - -- *Von:* ss [mailto:[EMAIL PROTECTED] *Gesendet:* Wednesday, October 08, 2008 5:00 PM *An:* Daniel Malter *Cc:* R help *Betreff:* Re: [R] How to join the two tables based on one overlapped column Dear Daniel, Thank you

[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 want

[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

[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] 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 have a matrix: dim(data1) [1] 34176

[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

Re: [R] Problem with rowMeans()

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 'data', which looks like: data[1:4,1:4] Probe_ID Gene_Symbol M1601 M1602 1 A_23_P10586213CDNA73

Re: [R] Problem with rowMeans()

] 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.names = NULL ,header=TRUE, fill=TRUE) looks like you have a data frame

Re: [R] Problem with rowMeans()

[EMAIL PROTECTED] wrote: ss wrote: Hi Wacek, Yes, data is data frame not a matrix. is.numeric(data[3]) [1] FALSE what is class(data[3]) But I looked at the column 3 and it looks okay though. There are few NAs and I did find anything strange. Any suggestions? Thanks

Re: [R] Problem with rowMeans()

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-1342561271_log2_with_symbols.txt', row.names = NULL ,header=TRUE, fill=TRUE) class(data[3]) [1] data.frame

Re: [R] Problem with rowMeans()

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 try your code soon. I did this first

[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 also

[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 -

[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 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) Warning

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

the lines that are not correct You might also try: read.table(a.txt, sep=\t, fill=TRUE) On Thu, Apr 24, 2008 at 8:32 PM, ss [EMAIL PROTECTED] wrote: 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

[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

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

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:[EMAIL PROTECTED] On Behalf Of ss Sent: Friday, April 11, 2008 11:23 AM To: r-help@r-project.org Subject: [R] How

[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: