a block so that I can not download
packages into R from CRAN. I want to download the package "limma". I
have downloaded and unzipped the limma zip file onto my desktop. How
do i install limma from my desktop into R ? Do I use...command ?
Please can someone tell me what to next to the prompt in R to enable
me to install the limma package from my desktop.
Thank you
Michael.
</div
Order by: Relevance
<div class="preformatted">There's been a name change for the function in the statmod package.
You get this
warning because you have re-installed the statmod package since Oct 20
but don't
yet have the corresponding limma version update. Try limma again
today (from
CRAN).
Gordon
> Date: Tue, 25 Oct 2005 23:08:05 -0400
> From: Naomi Altman <naomi at="" stat.psu.edu="">
…
div class="preformatted">The limma package has now forked into two series, one which depends on
R
1.9.0 and one which depends on R 1.7.1-1.8.1.
Limma versions...development package area. These versions are
developmental and
are not recommended to users.
Limma versions 1.3.X etc continue to depend on R 1.7.1 - 1.8.1 and are
being incremented at http://bioinf.wehi.edu.au/limma
div class="preformatted">Hi,
I just have a quick question. I have been using limma to create
toptables looking at differences betwen 6 groups. When I look at the
results of the toptables I assumed that...software but the FC was the opposite way
around. I have given an example below:
group1 - group2
in limma gene X = +, Y=+ and Z=-
in MEV gene X= - , Y= - and Z=+
Similar genes are detected …
the same way?
>
>For LimmaGUI, I use the latest (July 2005), version 1.3.9 (which uses
>limma 2.0.2) on R 2.1.1
>Limma, I am using version 2.2.0 with R 2.2.0 (both latest)
limma 2.2.0 was the version of limma at the time...of last Bioconductor
release, but it is not the latest version of limma. Actually limma
2.4.13 is available for R 2.2.0. Please read Section 2.2
(I…
div class="preformatted">Hello list members,
I was wondering if limma method can be used for spectral counts of
proteins from mass spectrometry. If yes, is there a function in
Bioconductor...that normalizes these counts.before running limma.
Thank you for your help,
Yolande
</div
div class="preformatted">Hello,
limma has been so valuable in microarray data analysis, but has anyone
used limma for finding differentially expressed proteins...proteins, and both tumor and normal have a number of
replicates. Could such data be analyzed with limma?
If limma can not be used here, what statistics method is suitable so
that we can get statistically significant proteins
updated 12.6 years ago • Yong Li
div class="preformatted">Hello,
I generated a topTable using limma package for illumine microarray
data analysis. Next I want to draw a heatmap based on the output of
limma. Could anyone
<div class="preformatted">
I have been looking for some examples of limma with Affymetrix data.
There
is a simple example in the documentation, but not a case study as with
the
dye swap experiments, and I am confused as to how to proceed with
using
limma on my data.
I need to eventually analyze a 2^4 factorial experiment, but I'd like
to
start with a smaller example so I can get...div clas…
div class="preformatted">Hello, everybody,
I'm doing some affy microarray analysis using limma, and I'm not a
statistician. I was told that I need to check if the model fits the
data before get the significant gene lists...So how should I do it in
limma? And is it really necessary? If not, why?
Thanks a lot!
Bin</div
updated 19.6 years ago • Ye, Bin
div class="preformatted">Hello,
My question is whether the package limma allows you to
run random effect models for each gene through the
lmFit function. I ran 6800 random effects models from...I
don?t know how to get the adjusted the p-values
because these models were ran in SAS and limma accept
only lmFit object.
Thanks for your help.
Hocine Tighiouart
Biostatistics Research Center
Instit…
<div class="preformatted">Hi,
I am using the limma package for an analysis of differential
expression and have a question about how the t-test in limma works. To
my understanding a difference between the usuall t-test and the one
used in limma is that the standard error in limma is calculated by
using a linear method based on a Bayesian model (I don't really get
how it works ).
In the use…
div class="preformatted">Dear limma expert,
I have a question about performing F-test (with several groups) on
limma.
If I have 3 targets (using Affy chips) called...H0: no difference vs. H1: at least one target is different,
(Similar with example on Section 8.6 of limma user guide at pp.42-43)
Should I construct my contrast matrix:
> makeContrasts(RNA2-RNA1, RNA3-RNA2, RNA3-RNA1) # wi…
div class="preformatted">Dermot,
The limma users guide has really been expanded over the years and
contains an excellent example of just what you need.
In R, do:
library...limma)
limmaUsersGuide()
then go to page 45 of the guide and read the whole section. I use the
treatment-contrast parameterization...a message you posed in the Bioconductor archives
> requesting info on 2 x2 factor…
<div class="preformatted">Dear all,
I recently encountered a problem subsetting limma TestResults on a
new Bioconductor install. If I do
> results<-decideTests(fit3,adjust="holm")
> results[results<0...div class="preformatted">Dear all,
I recently encountered a problem subsetting limma TestResults on a
new Bioconductor install. If I do
> results&…
updated 18.6 years ago • Michael Strehle
div class="preformatted">Just ANOTHER limma contrast matrix question:
I am trying to compute some contrasts of interest and have three
factors:
Treatment (Hypoxic...Kidney versus liver?
And the
effect of the KO as compared to WT in liver? I have looked at the
limma
guide and thought I had the idea, but this is slightly more
complicated than
the limma example given.
Thanks,
Sean
</div
div class="preformatted"> From what I can tell, the way to process Nimblegen data is use
limma. The latter does not read Nimblegen ".pair" files, so
you sort of glue together your own limma-friendly data structures
and...then let limma take over.
Is that about it?
Thanks,
Tom
</div
div class="preformatted">Dear members,
Is there any documentation on statistics used in limma package? How
should limma be cited in a publication.
Thanks
Sohail Khan
Scientific Programmer
COLD SPRING HARBOR LABORATORY
div class="preformatted">Hi all,
I just read on http://bioinf.wehi.edu.au/limma/ that
the latest stable version of the limma package is
1.8.17 dated 10 January 2005. It said I could find
this on Bioconductor
<div class="preformatted">Hello all,
Ive been searching the mail archives for about 2 hours without
any luck on
finding an answer to this problem. I was just wondering if there was
a way to
take the results that I obtained from limma and plug them into some
sort of
annotation package (such as annaffy). I am using affymetrix moe4302
gene chips
and would like to learn more about the g…
<div class="preformatted">Dear Pook,
At 01:57 AM 18/07/2003, Pook Veerachato wrote:
>Dear Dr.Smyth
>
>Thank you very much for a software website. I already installed it.
>However, I've some questions about using this software to ask you.
>
>I tried to import my datafiles from the program "Imagene"
(Biodiscovery)
>into R. Imagene datafiles ar…
div class="preformatted">I want to normalize for print order in limma, but I am running into
trouble using the function when method='plate' because:
Error in FUN(X[[1]], ...) : could not find function "huber...I am running R 2.4.1 and limma 2.9.17. Can someone supply me with the
function "huber" so the normalization function works? Is there
another work-around
updated 17.8 years ago • Erik Dopman
div class="preformatted">Dear Dr.Smyth,
I'm struggling with limma to apply it to two-group microarray data.
I thought ebayes() in limma shrinks the variance but not the "sign"
of the original...T statistic and the mean difference
in the gene 1(or the row 1).
I tried to follow example code in limma.
What seems to be problem here?
Thank you in advance.
Best,
Jihoon Kim
--------------------…
updated 19.5 years ago • Jihoon Kim
using the Benjamini
and
Hocberg fdr procedures in multtest or the p.adjust/topTable functions
in
limma.
I suspect that 0.05 is also too conservative
-----Original Message-----
From: Stephen Henderson
To: 'bioconductor@stat.math.ethz.ch...Sent: 08/12/03 13:49
Subject: [BioC] Limma parameters
I've been examining the eBayes function in Limma using some
affymetrix
data
we have. The default propor…
div class="preformatted">Hello Everyone!
I'm now working with my expression microarray data by limma to detect
differential expression probes. I have biology as my knowledge
background ,not statistics, so I'm confused...with the design matrix and
contrast matrix in the limma usersguide. now i have read the target
file
as follows:
SlideNumber FileName Cy3 Cy5
1 1 15_1_3.txt …
updated 13.7 years ago • sense_0109
gt; From: "Alessio Venier" <0509388V at student.gla.ac.uk>
> Subject: [BioC] problem with limma and BlueFuse
> To: bioconductor at stat.math.ethz.ch
>
> Hi,
>
> I've a problem using limma with bluefuse output files...gt; one file using a "target" file, I receive an error message.
> I've installed R 2.3.1 and limma 2.7.3
>
&…
<div class="preformatted">Hi,
I'm having trouble installing limma. I have R version 2.10. This is
the
error message I keep getting:
> source("http://bioconductor.org/biocLite.R")
Warning messages...div class="preformatted">Hi,
I'm having trouble installing limma. I have R version 2.10. This is
the
error message I keep getting:
> source("http://bioconductor.org/biocLite.…
<div class="preformatted">Dear Sam,
Yes, you can test any comparison.
> Date: Sun, 11 May 2014 20:53:41 -0400
> From: somnath bandyopadhyay <genome1976 at="" hotmail.com="">
> Cc: "bioconductor at r-project.org" <bioconductor at="" r-project.org="">
> Subject: [BioC] limma all by all
>
> Hi,
> I have microarray data from 10 dif…
updated 10.7 years ago • Gordon Smyth
all:
Just follow up on my RNAseq analysis on the TCGA RSEM processed so-
called raw counts using limma-voom package as Dr. Gordon suggested due
to the issue of so-called RSEM raw counts but not true raw counts that
edgeR required...Date: Thu, 30 Jan 2014 03:07:56 +0000
> CC: bioconductor@r-project.org
> Subject: Re: [BioC] limma-voom
>
> Hi, Dr. Smyth:
>
&g…
updated 11.0 years ago • Ming Yi
smaller than your kinship graph would have
suggested.
However you can do an approximate analysis in limma. If you can
separate
the samples into family groups, then you can set family to be a
blocking
variable in limma (using the...block argument of the
duplicateCorrelation
and lmFit functions). limma will then estimate a within-family
correlation from the expression data and will use it for th…
updated 12.4 years ago • Gordon Smyth
<div class="preformatted">Dear all,
I do have a probably simple question, is running "vsn" in limma
(normalizeBetweenArrays) the same as running "vsn" in marray or
arrayMagic?
My Boxplots suggest that there is a difference and I was wondering if
someone can give me a hint why that might be.
My particular problem is that I would like to use the fact that my
probes are spotted in duplicates b…
updated 20.0 years ago • A.E.Schiel@lumc.nl
<div class="preformatted">Hi eveyone,
my name is Priscila, and I'm beginning to use Limma package to analyse
my
microarray data.
Could someone help me? I can't even start to analyse my data because I
can't
read my...div class="preformatted">Hi eveyone,
my name is Priscila, and I'm beginning to use Limma package to analyse
my
microarray data.
Could someone help me? I can't even start …
<div class="preformatted">Hi, I am trying to run limma under R following the User guide.
Everything Ok until I get the message at the end, and I can figure out
wich one is the error. Could anyone help me?
Thanks
Veronica
> library (limma)
> dir()
[1] "Data GPR" "ExpDescFile.xls"
[3] "M1.4 VI2.4 (5-10-07) VI" "M1.8 VI1.8 (5-25-07) VI"
[…
Gordon K Smyth <smyth@wehi.edu.au> wrote:
From: Gordon K Smyth <smyth@wehi.edu.au>
Subject: LogFC in Limma
To: bioconductor@stat.math.ethz.ch
Date: Friday, October 24, 2008, 8:58 PM
Dear Kevin,
After sending my previous reply...the
arrays.
Also, do you have quality weights in your data or blocks in your fit?
In these
cases, limma will compute weighted averages, which are not the s…
div class="preformatted">Hi
First off, let me say that i think limma is a quite brilliant package
and I use it a lot. However, one of the biggest obstructions to using
limma for the lay biologist...Because of the limitations of analysis of variance for my microarray
data, I would like to use limma. Is there any *more* documentation I
can look at that will tell me the steps to take to work o…
div class="preformatted">
Hi,
I have been using LimmaGUI for a while, and I am starting to use Limma
directly, and I was comparing the results I get with both methods, to
make sure I am doing things right.
The lists of genes...same way?
For LimmaGUI, I use the latest (July 2005), version 1.3.9 (which uses
limma 2.0.2) on R 2.1.1
Limma, I am using version 2.2.0 with R 2.2.0 (both latest)
In…
DynDoc" "gcrma" "genefilter"
[13] "geneplotter" "GenomicRanges" "hgu95av2.db" "limma"
[17] "marray" "multtest" "vsn" "xtable"
Please wait...
#skipped a bunch of output
Warning message:
In getDependencies(pkgs, dependencies...available, lib) :
packages 'GenomicRanges', 'limma' are not available
> biocLite("limma")
Using R version 2.12.0, bioci…
div class="preformatted">Hi Bioconductor users;
I have a general question about limma model.
In limma package, usually one linear model applies to all genes, and
error
variances from all genes are modified
in advance,
best
Alessandro
At 23.43 28/08/03 +1000, you wrote:
>Thanks to help from Isaac Mehl, limma now supports ArrayVision data.
The
>support is in limma 1.1.12.
>
>The data file attached by Isaac is read by
>
> read.maimages
re: getting started), they
were
extremely helpful. Now I have a more specific question about the limma
User's guide. In section 8.2 on the 2-sample w/reference method, the
plot commands reference an object "genelist" that points...of the
clones are sequenced and the rest have clone ID's.
By the way, most of the image links in the LIMMA User's Guide are
broken.
-Dennis
p.s. I'm working from a debi…
<div class="preformatted">Hello,
This is my first time to past my help here, after I got lost from a
couple of requests.
As suggested by professor Gordon Smyth, I am writing to get some help
on LIMMA package while I am trying to analyze my dual-dye microarray
data. Before wrote this email I have I tried following LIMMA guide but
still have several places unclear with LIMMA for my data.
The…
div class="preformatted">Hi
Firstly, I think limma is excellent and use it a lot, but some recent
results are a bit, erm, disappointing and I wondered if someone could
explain...one type of bacterium and the
other
a different bacterium, compared to one another directly. I used limma
to analyse this and got a list of genes differentially regulated -
great!
THEN another replicate experiment w…
div class="preformatted">hello all limma exprts,
I have started using limma to analyse some spotted microarray data
but have run into problems trying to read...the data files in.
From the limma guide, having specified the "files" , then using the
command:
RG<-read.maimages(files, source="genepix")
I get:
Read 7863scan3.gpr...version 3 with
7863scan3 being the first
I also tried …
updated 20.8 years ago • Bryce MacIver
div class="preformatted">
Hi,
R v 2.0.1 and Limma v 1.8.15
Can anyone please explain to me why I get this error when trying to
use
the background correct method normexp...others. Other backgroundCorrect methods
work
fine.
Code with error is below.
Thanks,
Helen
library(limma)
targets=readTargets()
myfun=function(x) as.numeric(x$Flags>1)
RG=read.maimages(targets$FileName, source="gen…
<div class="preformatted">
Dear colleagues,
Hi, I would like to ask a question related to creating design matrix
in
limma. Statistics is not my strong subject so I apologise in advance
if
this is a silly question. I have a number of arrays with 3 different
treatments and I can generate a design matrix using modelMatrix.
> modelMatrix(targets, ref="Pool")
Found unique target names:
…
have thousands samples from different families. Now I want to find
differential expressed gene using Limma. I have family correlation
matrix
from kinship, Is there any way I can include these correlation in
lmFit?
Thanks,
Jack
div class="preformatted">Dear Ming,
Limma borrows information between genes, whereas Genespring does not.
This gives limma more statistical power to detect...can be dramatic.
See Shirley Liu's primer published in Nature Genetics for a tutorial
on
what limma does and why it works:
http://www.nature.com/nbt/journal/v28/n4/abs/nbt.1619.html
For reasons that I don't understand...at r-project…
updated 13.1 years ago • Gordon Smyth
with 2 different classes UM and M(with
subcklasses M1 and M2)
.
I have fitted the linear model with limma for the coefficients UM, M1
and M2 and I have compared UM vs (M1+M2).I found a significant change
(adjuste p-value<0.0001...the SAM's genes I obtained a good clustering, with a good
separation between the two classes. For LIMMA's genes I couldn't
succed to obtain a good separation be…
updated 19.0 years ago • daniela.marconi@libero.it
trying to normalize within arrays, an error with the
lowess
function was occurring. I checked the limma version and it was 2.9.7,
so we tried to install limma 2.12, but got a warning that the prior
version of limma cannot be removed...Oddly, the machine is in a state
such that if from the R GUI we choose Packages->Load Package, limma
does
not appear on the list (which makes sense because …
div class="preformatted">Dear Philipp,
Thanks for the bug report. Now fixed in limma 2.14.2. If you wait a
day,
you should be able to re-install limma from Bioconductor to get the
fix.
The bug was unfortunately...introduced when I tried to "streamline" the
plotMA() code in limma 2.13.6.
> Date: Tue, 20 May 2008 23:07:27 +0200
> From: Philipp Pagel <p.pagel at="" wzw.tum.d…
Hello,
I am using limma package to get the differential gene expression between two groups of the sample run on HGU133 PLUS 2.0 Affymetrix...data by Mas5 Algorithm. Can you please suggest me the step by step analysis of data using limma package?
Also how to define the two group when I am designing a linear fit model in limma
updated 5.8 years ago • singhjay
<div class="preformatted">Dear David,
I don't know what the problem is here, but it is unlikely to have
anything to do with missing
values in your data.
1. Does you data object contain any real data? Try
summary(exprs(myEset))
2. What version of R and limma are you using? (Every person who posts
a question to this list
should be giving this information routinely.) If you upgrade to…
div class="preformatted">limma User's Guide, Section 8.3 "Paired samples".
Adding covariates is no problem.
Best wishes
Gordon
> Date: Thu, 31 Jul 2008 11...33:12 -0400
> From: "Chunyan Liu" <chunyan.liu at="" cchmc.org="">
> Subject: [BioC] Can limma be used to the matched data?
> To: <bioconductor at="" stat.math.ethz.ch="">
> Message-ID: &am…
Thanks for pointing out the problem with reading quantarray files.
The bug has now been fixed in
limma 2.9.1. limma now reads the annotation columns for quantarray
files as well.
Best wishes
Gordon
> Date: Wed, 4 Oct 2006 09...43:50 +0100
> From: "Gavin Kelly" <gavin.kelly at="" cancer.org.uk="">
> Subject: Re: [BioC] Limma and Quantarray files
> To: <bioco…
updated 18.3 years ago • Gordon Smyth
div class="preformatted">Hi,
I miss the Amean field in the output of eBayes() in limma 2.9.10 .
It is there in limma 2.8.1
sample code:
# Simulate gene expression data,
# 6 microarrays and 100 genes with one gene...Ordinary t")
abline(0,1)
# Moderated t-statistic
eb <- eBayes(fit)
# this returns FALSE with limma 2.9.10, TRUE with limma 2.8.1
"Amean" %in% names(eb)
I run R 2.4.…
<div class="preformatted">Using both mouse and human Sentrix-6 beadarrays, I've managed to
normalize the arrays both with the beadarray package and the
BeadExplorer package. However, despite being able to get an exprSet
from beadarray and a BeadSummaryList from BeadExplorer, I'm not sure
how to go to Limma from there.
The exprSet does contain normalized values for all of the arrays, and
I…
updated 18.4 years ago • Anand Patel
div class="preformatted">I have a question about limma topTable output. What does the number in
the first colum represent for? Is there a way to match these numbers
to
affy_ids
for
filtering in conjunction with limma. Quite the opposite, your paper
concludes (incorrectly IMO) on its final page that limma needs to be
used
unfiltered.
In...probes from regular expressed probes. It is desirable to get rid
of
these atypical probes so that limma can concentrate on the behaviour
of
probes of genuine interest.
Filtering by mean log-intensity does not cause any...for the
lim…
updated 11.6 years ago • Gordon Smyth
<div class="preformatted">
Hi Gordon and everyone
I'm having difficulty running the background correction function in
LIMMA
I'm trying to use the "minimum" option but get the following error
message:
> AR123rep6RGback <- backgroundCorrect(AR123rep6RG...Hi Gordon and everyone
I'm having difficulty running the background correction function in
LIMMA
I'm trying to use the "mi…
div class="preformatted">
>[BioC] Limma User Guide: normalizeBetweenArrays
>Naomi Altman naomi at stat.psu.edu
>Fri Jul 15 22:50:39 CEST 2005
>
>Is there...a mistake on p. 67 of the Limma User's Guide (27 October
2004)?
>
>Firstly, MA.pq is not defined, but the density is plotted.
>Secondly, we have normalizeWithinArrays...Yes, there were…
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