Hello List
I have been asked to analyse some data for a colleague. The design consists of
a two sets of animals
First set of three - one leg is treated and the other is not under two
different conditions (control & overload are the same animals - control leg is
control (!) for treated leg;
Hello List
I was wondering if it is possible to make the individual 'tiles' in a heatmap
larger. Often when I plot heatmaps and want to label the rows with eg gene
names I either have to shrink the text or leave it out altogether as it becomes
so small as to be unreadable. I wondered if there w
Hello List
I have a list question. I'm doing some data wrangling for a colleague and I
have nested list in the following format:
structure(list(MU10 = structure(c(0.80527905920989, 0.4350488707836,
0.455195366623, 0.565174432205497, 0.208180556861924), .Names = c("MU.16",
"MU.19", "MU.21", "
Hi List
I have a dataframe (~1,200,000 rows deep) and I'd like to conditionally reorder
groups of rows in this dataframe.
I would like to reorder any rows where the Chr.Strand column contains a '-' but
reorder within subsets delineated by the Probe.Set.Name column.
# toy example
library
Hi Phil
That's it. Thanks.
Will have a read at the docs now and see if I can figure out why leaving the
'r'ead instruction out works. Seems counter-intuitive!
Best
Iain
From: Phil Spector
To: Iain Gallagher
Cc: r-help
Sent: Thursday, 31
'x.txt', 'r')
zT <- read.table(z, header=FALSE, sep='\t')
Error in read.table(z, header = FALSE, sep = "\t") :
seek not enabled for this connection
As I said in my previous email readLines fails as well. Rather strange really.
Anyway, as before an
Hi List
I have a series of zip archives each containing several files. One of these
files is called goCats.txt and I would like to read it into R from the archive.
It's a simple tab delimited text file.
pathToZip <-
'/home/iain/Documents/Work/Results/bovineMacRNAData/deAnalysis/afInfection/comm
I followed this case while it was ongoing.
It was a very interesting example of basic mistakes but also (for me) of
journal politicking.
Keith Baggerly and Kevin Coombes wrote a great paper - "DERIVING
CHEMOSENSITIVITY FROM CELL LINES: FORENSIC BIOINFORMATICS AND REPRODUCIBLE
RESEARCH IN H
Hi Eleni
Question like this are better served on the bioconductor mailing list.
Nonetheless try this
ALL <- topTable(fit2, coef=1, number=Inf)
ALL$SYMBOL <- unlist(mget(ALL$ID, hgu133plus2hsentrezgSYMBOL, ifnotfound=NA))
Here ALL is the output from limma for differential expression (ALL$ID is t
Dear List
I am trying to draw a heatmap using ggplot2. In this heatmap I have faceted my
data by 'infection' of which I have four. These four infections break down into
two types and I would like to reorder the 'infection' column of my data to
reflect this.
Toy example below:
library(ggplo
Above the graph on the left there are back and forward arrows. You can use
those (like a browser).
This might have been better asked on the R-Studio forums. They're very friendly.
best
iain
--- On Tue, 30/8/11, Eran Eidinger wrote:
> From: Eran Eidinger
> Subject: [R] R-Studio Question
> To
Hi Giovanni
Using Ubuntu and MacOSX may not be irrelevant. I use Ubuntu and if I carry out
a fresh install (e.g. after a new release - although I've stuck with 10.04 so
far) then I always have to mess around, check the web etc to install external
packages that R libraries I want to use rely on.
oops last reply was only half the solution:
library(plyr)
df <- data.frame(gene=c('A', 'A', 'E', 'A', 'F', 'F'), probe = c(1,2,3,4,5,6),
exp = c(0.34, 0.21, 0.11, 0.21, 0.56, 0.81))
ddply(df, .(gene), function(df)c(length(df$gene), median(df$exp))
gene V1V2
1A 3 0.210
2E 1 0.110
Hi Max
Using plyr instead of rehsape:
library(plyr)
df <- data.frame(gene=c('A', 'A', 'E', 'A', 'F', 'F'), probe = c(1,2,3,4,5,6))
ddply(df, .(gene), function(df)length(df$gene))
gene V1
1A 3
2E 1
3F 2
best
iain
--- On Thu, 30/6/11, Max Mariasegaram wrote:
> From: Max Mar
lt;- median(as.numeric(intervalsMonths))
Best
iain
--- On Wed, 29/6/11, Iain Gallagher wrote:
> From: Iain Gallagher
> Subject: [R] median time period
> To: r-help@r-project.org
> Date: Wednesday, 29 June, 2011, 16:24
> Hello List
>
> I'm trying to calculate the median
Hello List
I'm trying to calculate the median period (in months) of a set of time
intervals (between two interventions).
I have been playing with the lubridate package to create the intervals but I
can't think of the right approach to get the median timeperiod.
Toy code:
library(lubridate)
t
The first line of this reply is a definite candidate for the fortunes package!
best
i
--- On Thu, 17/3/11, bill.venab...@csiro.au wrote:
> From: bill.venab...@csiro.au
> Subject: Re: [R] Why doesn't this work ?
> To: ericst...@aol.com, r-help@r-project.org
> Date: Thursday, 17 March, 2011, 3:
This appeared today on the r-bloggers site and might be useful for you.
http://www.r-bloggers.com/release-of-xlconnect-0-1-3/
cheers
i
--- On Tue, 1/3/11, Steve Taylor wrote:
> From: Steve Taylor
> Subject: Re: [R] Export R dataframes to excel
> To: r-help@r-project.org, "maxsilva"
> Date:
Hi Darcy
This works for me:
Factor <- rep(factor(letters[1:4]), each = 10)
Size <- runif(40) * 100
par(mfrow = c(2, 2))
for (i in unique(Factor)) {
hist(Size[Factor == i], main = i,
xlab = paste("n =",length(Size[Factor == i])), ylab = "")
}
I think that using for (i in Factor) cycles through
','cumulMetric')
#return whole list
return(listMetric)# dataframe
}
Cheers
i
--- On Sat, 18/12/10, cstrato wrote:
> From: cstrato
> Subject: Re: [BioC] problem with function
> To: "Iain Gallagher"
> Cc: "bioconductor"
> Date:
B.utf8 LC_NUMERIC=C
[3] LC_TIME=en_GB.utf8LC_COLLATE=en_GB.utf8
[5] LC_MONETARY=C LC_MESSAGES=en_GB.utf8
[7] LC_PAPER=en_GB.utf8 LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_GB.utf8 LC
Hello List
I'm moving this over from the bioC list as, although the problem I'm working on
is biological, the current bottle neck is my poor understanding of R.
I wonder if someone would help me with the following function.
cumulMetric <- function(deMirPresGenes, deMirs){
#need to match po
Keith
Download the netLabR package from
http://www.meduniwien.ac.at/user/georg.dorffner/netalg.html
i.e. download the .tar.gz or zip files. Inside these, in the inst/doc directory
you'll find two English manuals.
HTH
iain
--- On Thu, 25/3/10, Keith McMillan wrote:
> From: Keith McMillan
>
Best to send any comments on documentation to the author of the documentation.
iain
--- On Fri, 26/3/10, Xu Wang wrote:
> From: Xu Wang
> Subject: [R] where do I send typos?
> To: r-help@r-project.org
> Date: Friday, 26 March, 2010, 5:15
>
> Hi,
>
> I notice several typos when reading docume
these are vectors in R not lists
try:
a<-c('a', 'b', 'c')#first vector (like A)
> a
[1] "a" "b" "c"
b<-c('c', 'd', 'e')#second vector (like B)
> b
[1] "c" "d" "e"
c<-setdiff(b,a)# all those in B but not A
> c
[1] "d" "e"
cheers
iain
--- On Fri, 12/2/10, Zoppoli, Gabriele (NIH/NCI) [G]
wrote
sorry, misread your post
try this...
> c<-setdiff(a,b)
> c
[[1]]
[1] "a"
[[2]]
[1] "b"
for a list C that contains all the members in
the list B that are not in list A
--- On Fri, 12/2/10, Zoppoli, Gabriele (NIH/NCI) [G]
wrote:
> From: Zoppoli, Gabriele (NIH/NCI) [G]
> Subject: [R] logical
> a<-list('a', 'b', 'c')
> b<-list('c', 'd', 'e')
> c<-intersect(a,b)
> c
[[1]]
[1] "c"
Is this what you want?
Cheers
Iain
--- On Fri, 12/2/10, Zoppoli, Gabriele (NIH/NCI) [G]
wrote:
> From: Zoppoli, Gabriele (NIH/NCI) [G]
> Subject: [R] logical operations with lists
> To: "r-help@r-project
Hi Steve
Have you tried:
apt-cache search gfortran
in a terminal window.
Then
sudo apt-get install theRelevantPackage
I think you also need the Universe repos enabled.
HTH
Iain
--- On Tue, 8/12/09, steve_fried...@nps.gov wrote:
> From: steve_fried...@nps.gov
> Subject: [R] Upgrading To
Hi List
I have data in the following form:
Gene TFBS
NUDC PPARA(1) HNF4(20) HNF4(96) AHRARNT(104) CACBINDINGPROTEIN(149)
T3R(167) HLF(191)
RPA2 STAT4(57) HEB(251)
TAF12 PAX3(53) YY1(92) BRCA(99) GLI(101)
EIF3I NERF(10) P300(10)
TRAPPC3 HIC1(3) PAX5(17) PAX5(110) NRF1(1
Hello list
I have a problem with a dataset (see toy example below) where I am trying to
find the difference between two (or more numbers) and discard those
observations which fall outside a set interval.
An example and further explanation:
values ind
12655 7A5
23028
Hello list.
I am hoping for some help with a relatively simple problem. I have a data frame
arranged as below. I want to be able to count the occurrence of each gene (eg
let-7e) by Experiment. In other words how many times does a given gene crop up
in the dataframe. I tried table but couldn't
Hello list.
I have a vector of values:
eg
> head(diff_mirs_list)
[1] "hsa-miR-26b" "hsa-miR-26b" "hsa-miR-23a" "hsa-miR-27b" "hsa-miR-29a"
[6] "hsa-miR-29b"
and I would like to conditionally replace each value in this vector with a
number defined in a dataframe:
> fc
Probe ave.fc
Hi
I'm trying to install the RBGL package. However I am getting the following
error; can anybody shed some light on what I'm missing?
/usr/lib/gcc/i486-linux-gnu/4.1.2/../../../../include/c++/4.1.2/cstdlib:135:
error: â::systemâ has not been declared
Thanks.
Iain
> sessionInfo()
R vers
Hi Chibisi
I'm sort of jumping into this thread but from your description of charts /
plotting below I thought you might like to take a look at flot:
http://code.google.com/p/flot/
>From the page
"Flot is a pure Javascript plotting library for jQuery. It produces graphical
plots of arbitrary
Thanks for all the excellent replies.
Iain
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PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and p
Hello list
I have been given some Excel sheets with data laid like this:
Col1Col2
A 3
2
3
B 4
5
4
C 1
4
3
I was hoping to import this into R as a csv and then get the mean and SD for
each letter in
Hi Miklos.
If you want to install R packages to the /usr/lib/R/library directory you need
to start R with 'root' user privileges. Ordinary users do not have the
appropriate permissions to write to this directory. At the command line type:
sudo R
type your password when prompted.
You won't ne
I'm pretty sure I've had similar problems to this in the past and the problem
has been a badly formatted text file ie you think it's all tab delimited but
it's not.
I can't be more specific (because it's your file) but it would be worth copying
the non appearing rows into a separate file and se
Hi Zack.
I don't know how helpful this is but I use R on 64bit ubuntu for the analysis
of large microarray datasets. R may well be taking advantage of all your memory
but the objects it's creating are too big. You could run 'top' in another
terminal window to examine this behaviour. If R is usi
Hi list.
I have a numerical dataset 22,000 rows deep and 43 columns wide. I would like
to remove those rows which contain only values less than 100 (ie if any value
in the row is greater than 100 the row stays in the dataset). I am unsure how
to test each individual value across the rows and th
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