Hi
I am trying to make heatmaps first based of QTLs profile only and then
I want to cluster them based on Column only!!!
Expression QTLs heat map
heatmap.2(expression.qtl,Rowv=F,dendrogram="column",trace="none",
distfun = function(c) as.dist(1 - c), density.info="none",
trace="none", cexRow =
X959X967X968
X9591 -0.04 0.45
X967-0.04 1 -0.09
X9680.45-0.09 1
X968_2 0.76-0.16 0.82
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Hi
I want to do correlation of genes but I need to know p-values to
construct netwrok based on correlation. But I,m getting too many zero
for some reasons. I read one paper and they did analysed their data
by ::
1- R values
2-P-values
3-Spearman p values - FDR corrected (Bejamini-Hochberg)
Do yo
Hi
Could any one please help how I can trnasform data based on Box-Cox
Transformations. I have massive data set with many variables. If
possible someone can write few lines so I can read in all data set
once and transform it.
g1 g2 g2
97.03703704 89.25925926 4.4
24.9074
Hi
I have data set consisting of my many variables and also in some cases
missing values. I want to probit transformation of my whole data set
using library VGAM or any other possible way. I would appreciat if
some one can help in writing code for probit transformation
V1 V10 V11 V1
Hi
I used to make heatmaps using following commands but now some thing
has changed as I get
library(gplots)
heatmap.
2(qtl.map,Rowv=F,dendrogram="column",col=colorRampPalette(c("blue","lightblue","black","black","yellow","red")),breaks=seq(-4.01,4.01,length.out=51),
density.info="none", )
follow
, I
want to present the Hazard ratio, 95% CI, and p value for each combination of
the three variables. How do I get R to give me these values please?
I think that the contrast function does this for other models but does not work
for coxph?
Many thanks
Stuart Patterson
Royal Veterinary Coll
other constraints. I
imagine that something could be done with mathgraph.
Thanks,
Stuart
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PLEASE do
Francois
You might try the BB package, which has quite a nice example.
Stuart
On Sat, 19 Jul 2008 10:20:34 +1000, François Aucoin
<[EMAIL PROTECTED]> wrote:
Hey,
I was wondering if there existed a R function similar to 'fsolve' or
'fzero' Matlab function
/drampl/ ) or write your problem in
GAMS or AMPL format and submit to the Neos server either directly
(http://neos.mcs.anl.gov/neos/) or by using pyneos.py
(www.gerad.ca/~orban/pyneos/pyneos.py). I really hope this gets worked out
in R at some stage!
Stuart
On Sun, 20 Jul 2008 08:10:35 +1000,
?
> 64:70[-c(2, 4)]
[1] 64 65 66 67 68 69 70
Just wondering.
--
Stuart Luppescu -=- slu .at. ccsr.uchicago.edu
University of Chicago -=- CCSR
才文と智奈美の父 -=-Kernel 2.6.30-gentoo-r5
Cordelia: Hi! You having fun? Angel: Sure. This is,
uh... Cordelia: Your idea of hell.
and rnorm() doesn't include arguments for
skewness and kurtosis. kurtosis() functions exist in e1071 and
fUtilities, but they only return the kurtosis of the input data. Let me
know if you find something.
--
Stuart Luppescu
University of Chicago
__
right around 1.0.
Admittedly, this is a rather big job: lmer with 2,200,000 records
crossed by 125,000 students and 10,000 teachers. But I don't understand
why it should consume resources so avariciously when run as a BATCH job.
Can anyone explain this to me?
TIA
--
Stuart Luppescu -*-*- slu ccsr
d by ess under emacs. You can get
the same thing with R in ess by highlighting the code and pressing C-c
C-r (or C-c C-b to run the whole program).
--
Stuart Luppescu
University of Chicago
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e("Supervised: Mapping plot for", data)
>
> }
>
>
> #use the plotxyf function.
> plotxyf(final.xyf)
BTW, I think it's better not to use "data" as a function parameter,
since it has reserved use in the language.
--
Stuart Luppe
one. Shouldn't ddply() produce the same ?
Thanks in advance for your help,
- Stuart Andrews
> set.seed(1234)
> aa = as.data.frame(matrix(rnorm(100)>0.3,nrow=20))
> names(aa) = c('a','b','c','d','e')
> head(aa)
a b c
formula or character vector"
I assumed that I could select entire columns (i.e. the *variables*
that comprise my data.frame) using this argument.
Thx again,
- S.
On Apr 7, 2010, at 6:13 PM, Steve Lianoglou wrote:
Howdy,
I'm no plyr master, but here's my 2 cents ...
On Wed, Apr
Thanks Charles, for clarifying.
My statement holds for matrices, which are 2 dimensional. And, as you
mentioned, a single index implies vector indexing where the drop
argument doesn't make sense. I am somewhat relieved, given this new
understanding.
But I am still puzzled as to why R
fy for the locally-fitted estimate line?
Stuart
Dr Stuart J Leask DM FRCPsych MA BChir
Clinical Senior Lecturer and Honorary Consultant in Clinical Psychiatry
University Dept of Psychiatry, A Floor, Queen's Medical Centre,
Nottingham. NG7 2UH
www: Google "Dr Stuart Leask"
This mes
keywords: debug, do.call, "debugging in", suppress, arguments, list,
screen, console, output
Hi,
I would like to control the output to the console while debugging
functions that are called by do.call( FCN, ARGUMENTS ) when the
arguments are quite large. Is there a simple way to suppress
code I have written is as follows.
I would be ever so grateful for any advice anyone may be able to offer.
With best wishes,
Stuart Reece,
Australia.
useOuterStrips(hexbinplot(Transferin ~ Age | factor(Race) + factor(Sex), data =
NHANES, type = "r",
someone can help. My ugly code is below, with some data for testing.
Stuart
Dr Stuart John Leask DM FRCPsych MB BChir MA
Clinical Senior Lecturer and Honorary Consultant Pychiatrist
Institute of Mental Health, Innovation Park
Triumph Road, Nottingham, Notts. NG7 2TU. UK
Tel. +44 115 82 30419
stuart
Ah, no, my method does fail.
Consider an ID that has a duplicate DATE that isn't the first date, but it's
first date is the same as another ID's first date that IS a duplicate.
Test data is all - see below it failing.
So, I remain very grateful for your function!
St
n. I will compare the two
approaches (and assume that mine is flawed!).
Stuart
ID <- c(58,58,58,58,167,167,323,323,323,323,323,323,323
,547,794,814,814,814,814,814,814,841,841,841,841,841
,841,841,841,841,910,910,910,910,910,910,999,1019,1019
"167" "841" "1019"
Stuart
-Original Message-
From: PIKAL Petr [mailto:petr.pi...@precheza.cz]
Sent: 23 October 2012 13:15
To: Stuart Leask; r-help@r-project.org
Subject: RE: [r] How to pick colums from a ragged array?
Hi
Rui's answer brought me to m
ates, they are not the first
date.
-Original Message-
From: arun [mailto:smartpink...@yahoo.com]
Sent: 23 October 2012 14:29
To: Stuart Leask
Cc: R help
Subject: Re: [R] [r] How to pick colums from a ragged array?
Hi,
Also one more thing:
This should get the dates which are duplicated. In
frame list
[2,] 2 data.frame list
[3,] 2 data.frame list
This leaves me with the same problem I had with my ragged array i.e. how do I
put all the second elements from this long list of data frames, into a single
list?
I need to end up with a list of all the IDs that have duplicate first (or last
So I get my list of IDs to exclude from:
g.rr<-do.call(rbind, g.r)[1]
dim(g.rr)
g.rr[1:(dim(g.rr)[1]/2)]
Many thanks.
Stuart
-Original Message-
From: Rui Barradas [mailto:ruipbarra...@sapo.pt]
Sent: 23 October 2012 13:42
To: Stuart Leask
Cc: r-help@r-project.org
Subject: Re: FW:
iest/first date function, INCLUDE should be TRUE, apart from
FALSE for _all_ the instances of IDs 167, 841 and 1019
For the latest/last date function, INCLUDE should be TRUE, apart from FALSE for
all the instances of ID 323.
Stuart
-Original Message-
From: arun [mailto:smartpink...@yaho
INCLUDE.FIRST), then on a separate run to consider the
last date (to produce e.g. INCLUDE.LAST).
-Original Message-
From: arun [mailto:smartpink...@yahoo.com]
Sent: 25 October 2012 12:32
To: Stuart Leask
Cc: R help; Petr PIKAL
Subject: Re: [r] How to pick colums from a ragged array?
Hi
Many thanks!
Stuart
-Original Message-
From: arun [mailto:smartpink...@yahoo.com]
Sent: 26 October 2012 13:54
To: Stuart Leask
Cc: R help; Petr PIKAL
Subject: Re: [r] How to pick colums from a ragged array?
Hi Stuart,
I guess, this should do it.
fun1H<-function(dat){
res1H
ead100, read110, read111)
Isn't there an easier way to do this?
Thanks.
--
Stuart Luppescu
University of Chicago
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PLEASE do read the posting guide http://www.
06.0448 -6.98104 1.02349 0.65789 NANA NANA 100
524 215.9634 2.93754 0.37856 0.01297 NANA NA NA 100
--
Stuart Luppescu
University of Chicago
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which is /usr/lib64/R/bin/exec/R (don't know if
this is the same in Ubuntu). File then gives:
file /usr/lib64/R/bin/exec/R
/usr/lib64/R/bin/exec/R: ELF 64-bit LSB executable, x86-64, version 1
(SYSV), dynamically linked (uses shared libs), for GNU/Linux 2.6.9,
stripped
--
Stuart Luppescu -*-
em? If you can find the object files, you can test
them with file as before, for example:
file /usr/lib64/R/library/MASS/libs/MASS.so
/usr/lib64/R/library/MASS/libs/MASS.so: ELF 64-bit LSB shared object,
x86-64, version 1 (SYSV), dynamically linked, stripped
--
Stuart Luppescu -=- slu .at. ccsr.uc
the Journal of
Statistical Software focusing on psychometrics in R. It has a lot of
valuable information.
http://www.jstatsoft.org/v20
--
Stuart Luppescu -=- slu .at. ccsr.uchicago.edu
University of Chicago -=- CCSR
才文と智奈美の父 -=-Kernel 2.6.33-gentoo-r2
To paraphrase
provocati
Hi,
I was wondering if anyone knows of a package that contains the ability
for peak/valley detection. Here is an example of what I'm looking for,
only problem is that it's written in Matlab.
http://www.billauer.co.il/peakdet.html
Thanks for any help in advance.
-Joe
Never mind. I did find this package, which seems to do the trick. Thanks
http://rgm2.lab.nig.ac.jp/RGM2/R_man-2.9.0/library/msProcess/man/msExtrema.html
On Mon, Dec 13, 2010 at 9:05 PM, Joe Stuart wrote:
> Hi,
> I was wondering if anyone knows of a package that contains the ability
>
el
>
> On 14 December 2010 14:22, Joe Stuart wrote:
>> Never mind. I did find this package, which seems to do the trick. Thanks
>>
>> http://rgm2.lab.nig.ac.jp/RGM2/R_man-2.9.0/library/msProcess/man/msExtrema.html
>>
>> On Mon, Dec 13, 2010 at 9:05 PM, Joe S
r. I even tried this:
boxplot(meas.tab[,meas] ~ as.ordered(meas.tab$by.schl.plot.order)
but that didn't do any better. I would think people would want to do
this all the time. There must be an easy way to do it but I can't figure
it out. Can anyone help me?
--
Stuart Luppescu -=- slu .at. c
On Sun, 2011-01-23 at 17:37 -0600, Stuart Luppescu wrote:
[snip] Thanks to Ben and Dennis for their help, but right after I sent
the original message, I figured out how to solve my problem. I noticed
that boxplot() contains the at= argument. To get the box locations, I
used a line like this
e of the most prolific, unselfish, and
helpful contributors to this list. I often wonder how he finds time to
post all these enlightening comments and do his own work. You would be
better off to take advantage off his advice, and not spurn it.
--
Stuart Luppescu -=- slu .at. ccsr.uchicago.edu
it
> as from there.
Woah. That's really involved. I use this little shell function to
convert from ps to png:
function ps2png {
ps_file="$1"
png_file=`echo "$ps_file" | sed -e 's/\.ps$/.png/'`
gs -dQUIET -dNOPAUSE -dBATCH -sDEVICE=png16m -sOutputFi
le, entitled, "Fitting Value-added Models in R", by Harold
Doran, is relevant and very useful and interesting.
www-stat.stanford.edu/~rag/ed351longit/doran.pdf
--
Stuart Luppescu -=- slu .at. ccsr.uchicago.edu
University of Chicago -=- CCSR
才文と智奈美の父 -=-Kernel 2.6.33-gentoo-r2
producer);
exit(EXIT_FAILURE);
}
Unfortunately, I don't understand this at all. Can anyone give me a clue
as to what's happening?
Thanks.
--
Stuart Luppescu -=- slu .at. ccsr.uchicago.edu
University of Chicago -=- CCSR
才文と
simple, but thanks for writing anyway.
--
Stuart Luppescu -=- slu .at. ccsr.uchicago.edu
University of Chicago -=- CCSR
才文と智奈美の父 -=-Kernel 2.6.33-gentoo-r2
Have you ever wanted to write a book, but not known
where to start? Now is a very good time to jump
in, because the
Hi,
I'm trying to use the pipe function to read data from another process
on my server.
Here is the code I have tried.
con <- pipe("/var/matlab/scripts/stream.pl")
while(con_read <- readLines(con)) {
print(con_read)
}
Problem is that the data from the perl script just keeps appending to
con_re
Thanks for the info. I'll give that a try.
On May 25, 2010, at 5:36 PM, jim holtman wrote:
readLines will read until it reached an end-of -file. try
readLines(con, n=1)
to read one line at a time an then process it.
On Tue, May 25, 2010 at 2:07 PM, Joe Stuart
wrote:
Hi,
I
Hi,
I have a matrix with about 3000 rows, and 1 column. The contents of the matrix
are stock symbols (IBM, AAPL, etc) for instance. I also have a function that
takes a single stock symbol as an argument, parses the text of Google Finance
and returns the related stock symbols that the page has l
Hi,
I'm trying to write a file to a shared drive on a network. I use the
"write.csv" function with the correct path but R doesn't recognize the
directory. Is there something different I have to do since it's a shared drive?
Thanks.
[[alternative HTML version deleted]]
B + 0, data = t,
drop.unused.levels = TRUE) : *
* variable lengths differ (found for 'secB')*
I thought the merge would match up dates in secA and secB, therefore making
the different lengths of secA and secB irrelevant.
Any ideas
Thanks
Stuart
*Stuart*
*t: 01483 212979
m: 07766 57
an only seem to
get the predictions for the 1st specified level of the grouping
variable. I promise that I have read the documentation, and have tried a
number of things, but cannot get the correct predictions.
Thank you for any help.
Yours - Stuart
--
/*-----
ns but with no success. Can someone
give me some pointers?
Thanks.
--
Stuart Luppescu -=- slu .at. ccsr.uchicago.edu
University of Chicago -=- CCSR
才文と智奈美の父 -=- Kernel 2.6.36-gentoo-r5
Lars Strand: Will R run under Windows Pocket PC? Brian D. Ripley: We
don't know! There are no binary ver
00 0. 0.
Can anyone explain this to me?
Also, is there an easier, less clumsy way to test for the existence of a
row in a data frame?
Thanks in advance.
--
Stuart Luppescu -=- slu .at. ccsr.uchicago.edu
University of Chicago -=- CCSR
才文と智奈美の父 -
On Tue, 2011-08-16 at 12:10 -0500, Stuart Luppescu wrote:
> but when I use the ifelse() as above, I get this:
>[,1] [,2] [,3] [,4]
> [1,] 0.0417 0.0417 0.0417 0.0417
> [2,] 0. 0. 0. 0.
Oh, I see. ifelse
For labelling a plot, I am trying to rotate a character string using
text() so that characters are upright and reading down, for example, ...
L
i
k
e
t
h
i
s
.
It appears that par crt does not work with text. Does anyone have any
other suggestions. Thanks!
Yours - Stuart Rosen
89576 5
> dim(ex10ss)
[1] 2189576 5
Nothing seems to have changed. I want all the rows with NA in removed.
I am clearly doing something wrong.
The only alternative I could find is pretty similar:
use <- complete.cases ( ex10 )
ex10ss<-ex10s[use,]
which leads to the same result.
logy!) to compare the radius with the
axes, the circle isn't radius 40; it is closer to 15...
I suspect there is a simple answer.
Stuart
This message and any attachment are intended solely for the addressee and may
contain confidential information. If you have received this message in erro
(Oh, and yes I've tried setting 'inches=F', but I then get a circle correct on
X axis, but too large on the Y axis.)
-Original Message-
From: r-help-boun...@r-project.org [mailto:r-help-boun...@r-project.org] On
Behalf Of Stuart Leask
Sent: 18 July 2012 11:03
To: r-hel
the list if it starts happening again.
Stuart
-Original Message-
From: Leask Stuart
Sent: 19 July 2012 10:59
To: r-help@r-project.org
Subject: RE: 'symbols' not plotting correct circle radii
(Oh, and yes I've tried setting 'inches=F', but I then get a circle
You're right - easily tested by just re-sizing the graphics box - sort of
counter-intuitive until I remember the clue is in the name - this generates a
CIRCLE, come what may...
Stuart
From: Sarah Goslee [mailto:sarah.gos...@gmail.com]
Sent: 19 July 2012 11:18
To: Stuart Leask
Cc: r-h
eping the levels with 0 counts:
$ rating.6 : 'table' int [1:4(1d)] 7 1 2 0
..- attr(*, "dimnames")=List of 1
.. ..$ : chr [1:4] "1" "2" "3" "4"
But I really want tables of the rows. Do I have to write my own function
to count the numbers
.
> > - attr(*, "dimnames")=List of 2
> > ..$ : NULL
> > ..$ : chr [1:10] "rating.1" "rating.2" "rating.3" "rating.4" ...
> >>
> >
> > notice it is just an integer array.
> >
> > Also if you h
odd, because if I use RB & LB from a different dataset, it works fine...
Stuart
*
*
Original problem:
> j<-0 # start an iteration counter
> while(j<30)
Hi,
I have a time series ts.score that gets created based on a function.
When I print the time series out it prints two rows, first the date
then the value.
2011-06-14
-1.25947868
The function gets called multiple times in my script and I'm trying to
append the time series to an object called ts.
I will. Thanks
On Fri, Oct 28, 2011 at 10:18 AM, David Winsemius
wrote:
>
> On Oct 28, 2011, at 10:32 AM, Joe Stuart wrote:
>
>> Hi,
>> I have a time series ts.score that gets created based on a function.
>> When I print the time series out it prints two rows, first
4 1523 1406
Now obsid.f only has 3 degrees of freedom and the sum of squares is
0.00. Could this be due to the unbalanced design?
If someone can explain this to me I would be very grateful.
--
Stuart Luppescu -=- slu .at. ccsr.uchicago.edu
University of Chicago
ing? Any suggestions?
SV
Stuart Vyse
Professor
Box 5621 web: http://www.stuartvyse.com
Department of PsychologyPhone: 860-439-2339
Connecticut College FAX 860-439-5300
New London, CT 06320 email: stuart.v...@conncoll.edu
Hi,
I have a list of numbers (classified as a list) that contains integer(0)
empty vectors. How do I convert those integer(0) into NAs? Thanks
[[alternative HTML version deleted]]
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ing M estimator does!)
I know, a health warning has to surround results that are differing a lot
simply due to exact parameters used, but it would be nice to confirm/deny
the lines are looking different for this reason.
Dr Stuart J Leask DM MRCPsych MA BChir
Senior Lecturer and Honorary Cons
but I
can't seem to find the right combination of order/sort/sample + runif.
I fear it can't be that hard - has anyone cracked this?
Stuart
Dr Stuart J Leask DM MRCPsych MA BChir
Clinical Senior Lecturer and Honorary Consultant in Clinical Psychiatry
University Dept of Psychiatry, A
.
The code I have written is as follows.
I would be ever so grateful for any advice anyone may be able to offer.
With best wishes,
Stuart Reece,
Australia.
useOuterStrips(hexbinplot(Transferin ~ Age | factor(Race) + factor(Sex),
data = NHANES, type = "r",
appreciate any advice.
Many thanks
Stuart Barker
J.S.F. (Stuart) Barker HonDSc FTSE
Emeritus Professor
School of Environmental and Rural Science
University of New England
Armidale, NSW 2351
Australia
Honorary Professor
School of Integrative Biology
University of Queensland
Brisbane
HOME: 114
the three variables. How do I get R to give me these
values please?
I think that the contrast function does this for other models but does not
work for coxph?
Grateful for any suggestions
Best wishes
Stuart Patterson, Royal Veterinary College, University of London
[[alternative HTML vers
ow is how I feel that I ought to present my results. If anyone
has any suggestions on how to obtain these values I would be very grateful!
Cheers
Stuart
Variable
Hazard Ratio
95% Confidence Interval
p Value
Year
Prev. TB
Age
2002-2005
No
< 24 months
24-48 months
>48 months
Yes
< 2
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