Displaying 20 results from an estimated 1000 matches similar to: "Compression of largish expression array files in the DAAGbio/inst/doc directory?"
2012 Jan 24
1
Failure to get compactPDF to compact a pdf file
I am failing to get compactPDF to make any change to a pdf file
that, a/c to the message from the CRAN upload site, can be very
substantially compacted. Any ideas what may be wrong?
I have also tried recreating the pdf file. I also tried
R CMD build --resave-data --compact-vignettes DAAG
The data files compact alright (but I get the 'significantly better compression'
warning message
2007 Sep 23
3
html help fails for named vector objects (PR#9927)
help(letters, htmlhelp=TRUE) fails.
Under the Mac OSX gui, the message is 'Help for the topic "a" was not
found.' Under the version documented below, and under Windows, the
message is
"No documentation for 'a' in specified packages and libraries:"
repeated for all the elements of letters, then followed by
"you could try
2004 Oct 19
1
Error in grep
Hi, there.
I used the function read.maimages in limma package to analyze the microarray data .but I got following message
>RG <- read.maimages(targets$FileName, source="spot")
Error in grep(pattern, x, ignore.case, extended, value, fixed) :
invalid argument
I don't know what is the matter
Thanks a lot
Regards
Shizhu Zang
Department of Biochemsitry
Peking
2011 Jun 07
1
Error message
Hi
fn <- dir(pattern="txt",full.name=T)
> fn
[1] "./GSM696980_US81503234_252741110209_S01_CGH_107_Sep09_1_1_32914.txt"
[2] "./GSM696981_US81503234_252741110209_S01_CGH_107_Sep09_1_2_32916.txt"
[3] "./GSM696982_US81503234_252741110209_S01_CGH_107_Sep09_1_3_33021.txt"
[4] "./GSM696983_US81503234_252741110209_S01_CGH_107_Sep09_1_4_33024.txt"
2007 Jul 08
2
how to revert to an older limma version?
Dear Sirs,
How can I revert to an older limma version?
Typing "install.packages("limma")" in R gives a list of mirrors. How
can I install the version I want after I obtain and untar the file (e.g,
limma_2.9.1.tar.gz)?
I am running R 2.5.0 on a Linux machine (CentOS 5). When using limma it
will not go past the read.maimages command.
I get this error:
Error in
2006 Jan 12
4
Loading Excel file into Limma
Dear mailing group,
This is my first time here. Glad to have this resource!
I am currently trying to load an Excel file into R (limma package loaded)
using the source(*name of directory*) command, but it cannot open the file.
I renamed the file as .R and .RData, to no avail. The Excel data contains
one gene name per row and about 100 data points per gene (columns).
I am only used to
2005 Oct 13
1
arima: warning when fixing MA parameters.
I am puzzled by the warning message in the output below. It appears
whether or not I fit the seasonal term (but the precise point of doing
this was to fit what is effectively a second seasonal term). Is there
some deep reason why AR parameters
("Warning message: some AR parameters were fixed: ...")
should somehow intrude into the fitting of a model that has only MA
terms?
>
2005 Dec 01
1
maImage() and layout()
Dear all,
Trying to produce 4 maImage plots (marray package) on the same device (2 on
the top and 2 on the bottom) with the layout() function or the split.screen()
function, we are facing the following problem:
it seems that maImage() does nt care about any of these 2 functions, and
plots only one image at a time.
Maybe this is inherent to this maImage() function, but we did not find
anything
2010 Nov 15
2
L-shaped boxes with lattice graphs?
Can anyone suggest an equivalent, for lattice graphs,
of the base graphics argument bty="l"?
NB that I am leaving off the box around the strip,
with a strip function:
stripfun <- function(which.given,which.panel,
factor.levels=as.expression(levlist), ...){
panel.text(x=0, y=0.5,
lab = as.expression(levlist[which.panel[which.given]]),
2004 Nov 10
1
Additions to the datasets package?
I have posted, at http://wwwmaths.anu.edu.au/~john/r/newsets/
image (.rda) files, and first stabs at .Rd files for various data on
deaths in London from 1629 to 1939. (There are of course gaps.)
The sources (Guy 1882 & Stocks 1942) are documented in the
.Rd files:
(1) poxetc: measles, smallpox & total deaths: 1629-1881
[I have deliberately left several inconsistencies that were
in
2008 Jun 02
0
RE: Largish filesystems [was Re: XFS install issue]
Alain Terriault wrote:
> Just wondering if any one ever consider/use Coraid for massive storage
> under CentOS?
> http://www.coraid.com
> It seems like a very reasonable option.. comments ?
I have one of those installed on CentOS 4.6 with 1TB of storage. I'm
sharing it between three servers. I can't say how well it works for
multi-TB storage, but it works well enough for me
2008 Jun 02
2
Largish filesystems [was Re: XFS install issue]
On Mon, Jun 2, 2008 at 2:03 PM, Johnny Hughes <johnny at centos.org> wrote:
> I would also not use XFS in production ... but that is just me.
Interesting, I thought that XFS was fairly safe for use. What would
you recommend for filesystems in the 50-500 terabyte range?
(And yes, we do actually run a 70 TB at the moment, so I'm not asking
just to annoy you; I'm genuinely
2004 Nov 21
1
Location of grobs etc on lattice output
Is there any way, after use of print.trellis(), to obtain the
co-ordinates of the plot region, e.g., in what are then the
native co-ordinates?
e.g.
library(DAAG)
library(lattice); library(grid)
data(cuckoos)
pushViewport(viewport(layout=grid.layout(2, 1)))
pushViewport(viewport(layout.pos.row=1))
cuckoos.strip <- stripplot(species ~ length, data=cuckoos)
print(cuckoos.strip,
2011 Mar 04
4
cv.lm syntax error
Dear all,
I've tried a multiple regression, and now I want to try a cross-validation.
I obtain this error (it must be sth related to df) that I don't understand,
any help would be appreciated.
cv.lm(df= dat, lm2.52f, m=3)
Error en `[.data.frame`(df, , ynam) : undefined columns selected
lm2.52f is my lm object, dat is a dataframe where the variables involved in
.lm are
I tried CVlm
2005 Apr 23
3
Enhanced version of plot.lm()
I propose the following enhancements and changes to plot.lm(),
the most important of which is the addition of a Residuals vs
Leverage plot.
(1) A residual versus leverage plot has been added, available
by specifying which = 5, and not included as one of the default
plots. Contours of Cook's distance are included, by default at
values of 0.5 and 1.0. The labeled points, if any, are those
2008 Jun 02
2
RE: Largish filesystems [was Re: XFS install issue]
To start I wish to that you for the swift response on this
issue. I do not think that I would get such a quick
response from a proprietary (closed-source) company. Open
Source :-).
To respond to one the comments about large file systems
?recommend you split it in several smaller (2-4TB)
filesystems ?
This is not feasible in many situations. In some
situations 2-4TB is not even a reasonable
2012 May 23
2
File format for single channel analysis of Agilent microarray data in Limma?
Hi,
I am following the protocol outlined here for analysis of single channel
Agilent microarray data:
http://matticklab.com/index.php?title=Single_channel_analysis_of_Agilent_microarray_data_with_Limma
I keep getting the following error message when using Limma's read.maimages
function to load my data into an RGList object:
Error in RG[[a]][, i] <- obj[, columns[[a]]] :
number of
2011 Feb 04
1
keep.source when semicolons separate statements on the one line
The following is 'semicolon.Rnw'
> \SweaveOpts{engine=R, keep.source=TRUE}
>
> <<xycig-A, eval=f, echo=f>>=
> library(SMIR); data(bronchit); library(KernSmooth)
> @ %
>
> Code for panel A is
> <<code-xycig-A, eval=f, echo=t>>=
> <<xycig-A>>
> @ %
Sweave("semicolon") yields the following 'semicolon.tex'
2006 May 25
1
Question regarding reading arrayvision files in limma
Hi Everyone,
I have been trying to read some Arrayvision files( 2 channel cDNA) and
am having some
problem. My code is :
setwd('C:/work/data/limma/ndd1');
files <- c('ndd1_1.txt','ndd1_2.txt','ndd1_3.txt');
RG=read.maimages(files,"arrayvision",sep="\t");
#Normalisation
MA=normalizeWithinArrays(RG);
#plotPrintTipLoess(MA);
#Fit Linear
2010 Nov 25
1
\Sweaveopts error
I have a file 4lmetc.Rnw, intended for inclusion in a LaTeX document,
that starts:
\SweaveOpts{engine=R, keep.source=TRUE}
\SweaveOpts{eps=FALSE, prefix.string=snArt/4lmetc}
The attempt to process the file through Sweave generates the error:
> Sweave("4lmetc")
Writing to file 4lmetc.tex
Processing code chunks ...
1 : keep.source term verbatim
Error in file(srcfile$filename, open =