801510L, 230957584L,
> 237932418L, 65724492L, 65879898L, 67718674L, 68318411L, 68454651L,
> 68567494L), s1 = c(-1L, -1L, -1L, -1L, -1L, 0L, 0L, 0L, 0L, 0L,
> 0L, 0L, 0L, 0L), s2 = c(0L, 0L, 0L, 0L, 0L, -1L, -1L, -1L, 1L,
> 1L, 0L, 0L, 0L, 0L), Count = c(1, 1, 1, 1, 1, 1, 1, 1, 1, 1,
>
uot;)
> )
> }
>
> do.call("rbind", lapply(lapply(split(df, paste(df$s1, df$s2)), f),
> unique))
>
>
> On 24/12/2007, affy snp <[EMAIL PROTECTED]> wrote:
> > Thanks Moshe! I apologize for not being so clear about the
> > second part. Again,
; M[-which( M$s1 == 0 & M$s2 == 0),]
>
> For the second question, you must start with the more
> precise definition of the grouping criterion.
>
> --- affy snp <[EMAIL PROTECTED]> wrote:
>
> > Hello list,
> >
> > I have a data frame M like:
> >
> >
Hello list,
I have a data frame M like:
BAC chrpos s1 s2
RP11-80G24177465510-10
RP11-198H14178696291-10
RP11-267M21179681704-10
RP11-89A19 180950808-10
RP11-6B16182255496-10
RP11-21
Dear list,
I have a matrix M (2500 rows and 9 columns). It looks like
2.2 0.1 2.63.6 ..
0.4 1.9 2.74.2..
1.8 2.5 4.32.2...
.
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]=
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
Thanks James!
Allen
On Dec 6, 2007 9:21 AM, James W. MacDonald <[EMAIL PROTECTED]> wrote:
>
>
> affy snp wrote:
> > 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 ori
entist - Pacific Northwest National Lab
>
> On Dec 5, 2007 4:20 PM, affy snp <[EMAIL PROTECTED]> wrote:
>
> > 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 orde
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 HTM
#x27;green','blue'))
> levelplot(x,col.regions=Lab.palette(10))
>
>
> On Nov 30, 2007 7:58 PM, affy snp <[EMAIL PROTECTED]> wrote:
> > Hi Jim,
> >
> > Thanks but I imagine the transformed data would
> > not actually represent the pattern from t
im(old.data)
>
> and then plot it.
>
> On Nov 30, 2007 5:09 PM, affy snp <[EMAIL PROTECTED]> wrote:
> > 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
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 08, and mak
> 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
Thanks a lot, Petr.
Allen
On Nov 29, 2007 12:12 PM, Petr PIKAL <[EMAIL PROTECTED]> wrote:
> Hi
>
> I just guess what you want but maybe
>
> rownames(log2.ratios) <-log2ratios$Clone
>
> changes rownames and then you could get your output (after getting rid of
> first column).
>
> If you just want
hich would be three variables. So you
> need to define what is supposed to happen in these cases.
>
> On Nov 28, 2007 8:21 PM, affy snp <[EMAIL PROTECTED]> wrote:
> > Hi Jim,
> >
> > Thanks a lot! I would like the blanks to be read as NAs.
> > I tried
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
t;[EMAIL PROTECTED]> wrote:
> If the data is fixed field, then read.fwf. Else blanks are normally
> allowed delimiters. How do you want to interprete blanks? There are
> number of ways, none of which you have specified.
>
> On Nov 28, 2007 6:46 PM, affy snp <[EMAIL PROTECTED]&
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]]
__
R-help@r-project.org mailing list
https://stat.ethz.ch/mailman/listi
Hi list,
I used heatmap() and heatmap.2() to draw the dendrogram
and got error messages for both. They were:
heatmap(as.matrix(y3),col=rainbow(256),scale = "column");dev.off();
Error in hclustfun(distfun(x)) :
NA/NaN/Inf in foreign function call (arg 11)
Does anybody know how to correct this?
icht-
> Van: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED]
> Namens Jim Lemon
> Verzonden: donderdag 22 november 2007 11:21
> Aan: affy snp
> CC: r-help@r-project.org
> Onderwerp: Re: [R] Heatmap problem
>
>
> affy snp wrote:
> > Hi friends,
> >
> > I
Hi Jim,
The problem with color2D.matplot is that it cannot
do dendrogram which I want.
Thanks!
Allen
On 11/22/07, Jim Lemon <[EMAIL PROTECTED]> wrote:
>
> affy snp wrote:
> > Hi friends,
> >
> > I used heatmap(as.matrix(y2),col=rainbow(256),scale = "c
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]]
__
1:4]
[,1] [,2] [,3] [,4]
[1,] 43121 132913 1 792
[2,] 149264 178012 1 817
[3,] 237378 142083 1 819
[4,] 149002 130012 1 832
>
On 11/18/07, affy snp <[EMAIL PROTECTED]> wrote:
>
> Thanks all of you. It works.
>
> Have a good weekend!
>
> Allen
>
> On 11/18/07, Be
ov 18, 2007, at 1:54 PM, Henrique Dallazuanna wrote:
>
> > clones.info[order(clones.info$CHROMOSOME),]
> >
> > --
> > Henrique Dallazuanna
> > Curitiba-Paraná-Brasil
> > 25° 25' 40" S 49° 16' 22" O
> >
> >
> > On 18/11/2007, affy sn
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 414196
function. There are many different plot
> functions with different arguments, and which one you are using depends
> on what kind of object is 'Disease.FL'. If you don't know the class of
> the object, you can do this:
>
> class(Disease.FL)
>
> Julian
>
> af
Dear list,
I have a question about using plot().
I tried the code:
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
Thank you very much, Julian. I got it.
Best,
Allen
On Nov 14, 2007 2:38 PM, Julian Burgos <[EMAIL PROTECTED]> wrote:
> One way to do this is
>
> range(which(B[,2]==1))
>
> Julian
>
>
> affy snp wrote:
> > Hello list,
> >
> > I read in a
Dear list,
Hello! I have a question about how to print a label in the plot.
I am using the following code:
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
clinical Statistics
> >
> >
> >
> > -Original Message-
> > From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On
> > Behalf Of jim holtman
> > Sent: Wednesday, November 14, 2007 8:39 AM
> > To: affy snp
> > Cc: r-help@r-project.org
> &
Hello list,
I read in a txt file using
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
Thanks Jim and Ben.
Allen
On Nov 12, 2007 3:43 PM, Benilton Carvalho <[EMAIL PROTECTED]> wrote:
> it's defined in Biobase.
>
>
> On Nov 12, 2007, at 3:30 PM, affy snp wrote:
>
> > Thanks Jim. It is way simple. Great.
> > Is there any function like rowMed
7,] / myAvg
>
>
> On Nov 12, 2007 1:37 PM, affy snp <[EMAIL PROTECTED]> wrote:
> > Dear list,
> >
> > Hi! I have a table A, 238304 rows and 243 columns (representing
> > samples). First of all, I would like to pool a group of samples
> > from 48th column t
Dear list,
Hi! I have a table A, 238304 rows and 243 columns (representing
samples). First of all, I would like to pool a group of samples
from 48th column to 243rd column and take the average across
them and make a single column,saying as the reference column.
Second, I want to use each column o
nvert to matrix, get rid of first column
> > x <- as.matrix(x[,-1])
> > y <- as.matrix(y[,-1])
> > z <- mapply(function(a,b)mean(c(a,b), na.rm=TRUE), x, y)
> > dim(z) <- dim(x)
> > z
> [,1] [,2] [,3]
> [1,] 2.045
> [2,] 1.52 NaN
lumn
> > x <- as.matrix(x[,-1])
> > y <- as.matrix(y[,-1])
> > z <- mapply(function(a,b)mean(c(a,b), na.rm=TRUE), x, y)
> > dim(z) <- dim(x)
> > z
> [,1] [,2] [,3]
> [1,] 2.045
> [2,] 1.52 NaN
> [3,] 2.542
> >
0 3.33 4.00
>
Allen
On Nov 11, 2007 10:41 PM, jim holtman <[EMAIL PROTECTED]> wrote:
> What did your text files look like? It would appear that there was
> not a line feed on the last line of the file. Also what does 'str' of
> x and y show? It appears t
> > y
> [,1] [,2] [,3]
> [1,] NA44
> [2,]22 NA
> [3,]122
> > z <- mapply(function(a,b)mean(c(a,b), na.rm=TRUE), x, y)
> > dim(z) <- dim(x)
> > z
> [,1] [,2] [,3]
> [1,] 2.045
> [2,] 1.52 NaN
&g
Dear list,
I am new to R and very inexperienced. Sorry for the trouble.
I have two txt files and want to merge them by taking the average.
More specifically, for example, the txt file1, with row names and column names,
consists of 238000 rows and 196 columns. Each column corresponds
to a sample. T
ng with the input file you can think of?
Thanks!
Allen
On Nov 10, 2007 10:37 AM, Gabor Grothendieck <[EMAIL PROTECTED]> wrote:
> Thanks.
>
>
> On Nov 10, 2007 10:29 AM, affy snp <[EMAIL PROTECTED]> wrote:
> > Gabor,
> >
> > I will do it either later today or t
Ted Harding <[EMAIL PROTECTED]> wrote:
> On 10-Nov-07 14:25:32, affy snp wrote:
> > Dear list,
> > I am wondering how to log-2 based transform a matrix
> > with numeric values?
> > I tried > CGHlog2<-log2(CGH) but got an error. Then I
> > found for log2(x) i
ems (you haven't told us
> what type they are), so you will need GBs of RAM, and preferably a 64-bit
> OS. Otherwise you would be better off using a DBMS to store the data (see
> the Manual mentioned in my first para).
>
>
> On Fri, 9 Nov 2007, affy snp wrote:
>
>
Dear list,
I am wondering how to log-2 based transform a matrix with numeric values?
I tried > CGHlog2<-log2(CGH) but got an error. Then I found for log2(x) in R,
the x has to be a numeric or complex vector. Any method for a matrix?
Thanks a lot and have a good weekend!
Allen
>Error in Math.da
"), "from myfile")
> DF <- sqldf(stmt, file.format = list(sep = " "))
Error in summary.connection(get(fo, envir)) : invalid connection
>
How should I correct this?
Thanks!
Allen
On Nov 10, 2007 1:11 AM, Gabor Grothendieck <[EMAIL PROTECTED]> wrote:
> On Nov
BTW, sth like:
A<-read.table(file="243_47mel_withnormal_expression_log2.txt",
+header=TRUE,row.names=1,colClasses=c('factor', rep('factor',486)))
will do anything good?
Allen
On Nov 10, 2007 12:41 AM, affy snp <[EMAIL PROTECTED]> wrote:
> Yes, I am
x27;))
>
> You can extend the 'what' to the size of the column that you have; e.g.
>
> what=c(rep(c(list(''), list(0)), rep=243), list(''))
>
>
>
>
> On Nov 10, 2007 12:29 AM, affy snp <[EMAIL PROTECTED]> wrote:
> > Hi Jim,
> &
ed (Mb)
> Ncells 169954 4.6 35 9.4 35 9.4
> Vcells 3102277 23.77803840 59.6 7200206 55.0
> > object.size(x)
> [1] 2424
>
> This took about 7 seconds. You have about 40X more data, so it should
> be interesting to see how it scales up. The objec
Hi Jim,
Actually besides the first column which is character, half of the 486 columns
are character as well.
Thanks!
Allen
On Nov 10, 2007 12:29 AM, affy snp <[EMAIL PROTECTED]> wrote:
> Hi Jim,
>
> I tired scan() first and got
>
> > x <- scan(file="243_47me
; it on subsequent runs which should be fast.
>
> On Nov 9, 2007 11:39 PM, affy snp <[EMAIL PROTECTED]> wrote:
>
> > 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
comes in in
> row order if that is what your data file has, so you could just add
> dimensions of
>
> dim(x) <- c(487, 238305)
>
> rows and columns are transposed, but if you have enough memory, you
> can transpose them, or just leave the data as is, and change your
> pro
e is the file you are reading
> and what is its format? Have you considered a database with this
> amount of data?
>
>
> On Nov 9, 2007 11:39 PM, affy snp <[EMAIL PROTECTED]> wrote:
> > Dear list,
> >
> > I need to read in a big table with 487 columns and 238,
ould do
> >
> > A[,seq(1,dim(A)[2],2)]
> >
> > Julian
> >
> >
> >
> > affy snp wrote:
> > > Hi Julian,
> > >
> > > Thanks for the help!
> > >
> > > Best,
> > > Allen
> > >
> >
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
I figured that out. I appreciate!
Allen
On Nov 9, 2007 11:25 PM, Julian Burgos <[EMAIL PROTECTED]> wrote:
> No problem. Actually, I missed a comma. You should do
>
> A[,seq(1,dim(A)[2],2)]
>
> Julian
>
>
>
> affy snp wrote:
> > Hi Julian,
&g
Research Lab
> School of Aquatic and Fishery Science
> University of Washington
>
> 1122 NE Boat Street
> Seattle, WA 98105
>
> Phone: 206-221-6864
>
>
>
>
> affy snp wrote:
> > Dear List,
> >
> > Hi! I am wondering what is the simplest way to
Dear List,
Hi! I am wondering what is the simplest way to subset a portion of columns
from a matrix.
For example, there is a matrix A (238,304*243). What is the simplest
way to get a sub-matrix B which comprises of column 1, 3, 5, 7,9,...(odd column
number) from matrix A?
Thank you very much for
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