div class="preformatted">Hi All
I'm looking for an opportunity to learn limma in the USA. Does anybody
know about courses offered in limma? I've used basic limma, but am now
planning a more complicated...time-coure experiment and would like to
learn from limma experts. I'm interested in cDNA applications.
Cecilia McGregor
Post-Doc
Sweetpotato Breeding and Genetics Lab
JC Miller
Order by: Relevance
a function that is
a modification of the normalizeWithinArrays() with printtiploess
option of
the limma package.
We are spot quality control prior to normalization which results in
some
genes being dropped. Once that happens...grid, so that the print top loess
can
be performed.
So I have been looking for the source code for limma, but it seams to
be
unavailable since the package is distributed…
updated 20.3 years ago • Peter Wilkinson
div class="preformatted">
>[BioC] LIMMA
>Matt Settles mattsettles at moscow.com
>Mon Jan 30 19:10:12 CET 2006
>
>Hello all,
>
>I've found an issue in your...limma package concerning read.maimages
>
>First there appears to be two different latest versions out there
CRAN has...gt;limma 2.4.7 and bioconductor has 2.2.0 is 2.4.7 still …
div class="preformatted">I've had a few requests for updates to the limma package from people
who
are still using R 1.9.1 or earlier. Naturally it would be best to
update to
R 2.0.1 but, for those...who need it, I've put a slightly modified
version of
limma 1.8.13 built for R 1.9.1 for Windows at
http://bioinf.wehi.edu.au/limma/r1091/limma_1.8.13.zip. You need to
download...then use "install p…
div class="preformatted">statmod does not get installed along with limma. Even if I install
statmod manually, it does not load when limma is loaded (although it
does when it is needed). This problem...has persisted for several
generations of limma.
--Naomi
</div
div class="preformatted">Hello all,
I am a PhD student at University of Pisa.
I frequently use LIMMA package to handle gene expression microarray
data.
I have a question about spot copies management by LIMMA.
I know that...LIMMA needs all spots on the array are in the same number
of copy ( e.g. each spot in double ).
In my research group It is just starting...for each probe. Moreover there is…
div class="preformatted">Hi,
I have found a problem with the limma, limmaGUI combination: (v 1.7.1
limma,
and 1.2.1 GUI).
The latest install was used (downloaded from the limmaGUI site) to
install...reported that is was unable to read the
image processing files. I have used older versions off limma/limmaGUI
before
and this always worked. After trying several
things (changing files, renaming a…
<div class="preformatted">Hi Ming,
voom is part of the limma package. There is a voom case study in the
limma User's Guide with complete working code. It is the last case
study
in the users guide.
voom works fine with either counts, or fractional counts, or scaled
counts.
We are currently finalizing additional voom code to detect
differential
splicing. That code isn't in the public pa…
updated 10.8 years ago • Gordon Smyth
class="preformatted">Dear colleages,
I can not uderstand a result I have. I made t-permutations and LIMMA
to
find differentially expressed genes on the same
dataset. Is it posible I can have
a gene which is overexpressed using...t-permutations (t value = +
something)
and underespressed using LIMMA (Statistic= - something) ?
Sorry but I can not fully understand the LIMMA algorithm yet.
Many …
preformatted">Dear Gerhard,
There have been only two changes to the empirical Bayes calculations
in limma since the early days. These have been in limma versions
2.4.0 and 2.4.13.
The change in 2.4.0 was introduced to better...Gordon
At 04:30 AM 3/05/2006, Gerhard Thallinger wrote:
>Dear Gordon,
>
> I am using limma regularly to analyze our microarray experiments
&…
updated 18.5 years ago • Gordon Smyth
div class="preformatted">Hi, I have some questions about the data that the limma package can
work on.
If I have some preprocessed/normalized data of log2 ratios from
2-color
arrays, but not the raw signal...data, can I still use lmFit? A related
question is, can limma work on a subset of the data from an array? For
example, after normalization, I filter out some probes/spots. If I can
retrieve…
updated 19.6 years ago • He, Yiwen NIH/CIT
preformatted">I have a data set which pretty much duplicates the experimental design
of one of the limma examples, so I am using that with great results
:-D
There is one difference though - the limma example has no duplicate
spots...whereas my design does. So I did two runs of limma, one to
find
differentially expressed spots, the other to find differentially
expressed genes (I assume limma …
<div class="preformatted">Dear Erika,
limma doesn't explicitly handle irregular replicates. (In my lab, we
haven't had to work with any of the new generation of Agilent arrays
yet,
so haven't had to solve the issues with them.)
Your best bet may be to simply average over the replicates for each
probe,
after normalisation, and before using lmFit(). This is not hard, but
requires some pro…
updated 16.4 years ago • Gordon Smyth
div class="preformatted">Hi,
I'm learning to use Limma following your userguide. Where can I find
the
'targets.txt' used in 3.2 Sample Limma Session? I have not been able
to find
div class="preformatted">The limma change log is no longer linked to from the URL
http://bioinf.wehi.edu.au/limma but instead is distributed as part of
the...changelog by
using
the html help in R and choosing "browse directory" need the top of the
page
for limma. Alternatively you can type
file.path(.find.package("limma"),"doc/changelog.txt")
at the R prompt to see where it is.
Gordon
div class="preformatted">Hello lists,
I am using Bioconductor/Limma package to analyze microRNA arrays.
I have 7 replicate two-color arrays, 4 probe replicates each array.
Follow Limma procedures...two columns of value the same?
Did I calculate it mistakenly or something behind this during the
Limma procedures?
Could anyone kindly explain it?
Thanks.
Kevin
[[alternative HTML versi…
class="preformatted">Hi Bioconductor users,
This is a very naive question on exporting subsets in limma. But I am
not
very familiar with pogramming.
I am trying to work through the limma user guide Sec 8.8 "Time Course
Experiments...I am able to complete the limma analysis but I am stuck
after subsetting the genes to only include genes with adj. p values <
0.05
> fit2 = contra…
div class="preformatted">
Hello Limma Developers,
I got this error when calling ebayes after lm.series:
Error in ebayes(fit) : No residual degrees of freedom...in linear model
fits
I tried both limma 1.3.1 and 1.3.12. I appreciate your help.
thanks,
Ken Ninh</div
<div class="preformatted">Dear List,
Sorry to bring up this adjusted p value question about limma. I
searched mail
list but didn't find an answer.
I know limma use "p.adjust()" for multiple test correction. And if
there is only
one coefficent, the adjust p values results of limma's top table is
the same as
I directly apply p.adjust to the P.Value vector.
My question is that if we have se…
<div class="preformatted">At 08:00 PM 20/10/2005, bioconductor-request at stat.math.ethz.ch
wrote:
>Date: Wed, 19 Oct 2005 14:26:42 -0400
>From: Naomi Altman <naomi at="" stat.psu.edu="">
>Subject: [BioC] ANCOVA in limma
>To: bioconductor at stat.math.ethz.ch
>
>We would like to adjust our ANOVA-type analysis by using the
>covariate "ag…
div class="preformatted">Hello,
I've tried to install the latest stable version of Limma.
With "biocLite()" command I get Limma 2.9.8 but if I use the
"install.package" command I get Limma 2.8.1.
How can I get the latest...stable" version of Limma package?
With the following commands I get Limma 2.9.8 (Is it a stable
version?)
source("http://bioconductor.org/biocLite.R...biocLite(c("limm…
div class="preformatted">Hi,
there seems to be a problem with decideTests (limma package):
results<-decideTests(fit2, adjust.method="BH")
gives a table with probe IDs as row names if the methods "separate...however,
row names are missing. Is this a feature the purpose of which I do not
understand?
This is limma 2.6.2 and R 2.3.0
Best,
Georg
</div
div class="preformatted">Dear all:
I'm trying to use limma package. But my intensity data is not two-
colored, but single color(gray), like the following:
Gene1 2596.87 2429.06 2436.62...1022.47 1144.77
1078.31 1007.18 841.17
How should I do the normalization in Limma? Any guidance is
appreciated.
Chunrong</div
updated 21.3 years ago • cxd55@cwru.edu
2006 20:47:50 +0200
> From: Georg Otto <georg.otto at="" tuebingen.mpg.de="">
> Subject: [BioC] limma decideTests
> To: bioconductor at stat.math.ethz.ch
>
> Hi,
>
> there seems to be a problem with decideTests (limma...are missing. Is this a feature the purpose of which I do
not
> understand?
>
> This is limma 2.6.2 and …
div class="preformatted">Hi,
I want to ask some questions about limma package .
if my data is not log-transform, whether also could use "lmFit"
function?
thanks!
Chang
[[alternative HTML version
<div class="preformatted">Dear Marissa,
Section 3.2 is a hypothetical example. As the guide says, it's "a
quick
overview of what an analysis might look like". There are no files for
download. On the other hand, the five case studies at the end of the
User's Guide do give links to data files for download.
Best wishes
Gordon
> Date: Thu, 25 Feb 2010 10:28:57 -0800
> From: …
div class="preformatted">Dear Sir
There is a question whether could limma move out outliers, which
are
not consistently reproducible and has a disproportionately large
effect on
the statistical...microarray slide, so I will have 16
data
points for each gene. If there is outliers, could I use limma to
filter
them?
Waiting your reply.
Best regards.
Chen
</div
updated 19.3 years ago • ? ?
<div class="preformatted">Hi,
We have a microarray experiment of cDNA of 36 spotted arrays,
reference
design.
Two persons run the analysis with same code and the same data for
education purposes. One loaded limma package version
>sessionInfo()
R version 2.2.0, 2005-10-06, i386-pc-mingw32
attached base packages:
[1] "methods" "stats" "graphics" "grDevices" "utils"
"datasets"
[…
updated 18.9 years ago • Ron Ophir
div class="preformatted">Hi All,
With a *quick* search in the mailing list and through the limma PDF I
couldn't find any information on how to provide for a covariance
structure in limma (this is for a repeated measures...lme has "weights" and "correlation" arguments which should do the
job...can anyone enlighten me on limma's way of specifying covariance
structures?
Thanks in advance,
Jake…
replicates)
group4: spinal cord unamplified RNA (3 Affymetrix replicates)
I fed all data through to limma and specified the following contrasts:
contrast1: group1-group2
contrast2: group3-group4
contrast3: (group1-group2...quite nice showing in average more than 80% agreement.
However, if I only feed group1 and group2 to limma without the rest of
the
data and repeat contrast1. And separate to t…
updated 19.6 years ago • Ilhem Diboun
<div class="preformatted">Hi all,
I'm trying to get familiar with the limma package, but I've run into
something
I don't understand. After I load the package, if I type:
?normalizeWithinArrays
The documentation...div class="preformatted">Hi all,
I'm trying to get familiar with the limma package, but I've run into
something
I don't understand. After I load the package, if I type:
?nor…
updated 21.3 years ago • Paul Boutros
preformatted">Dear Gordon and BioC users,
I have recently updated R and BioC packages (R.2.3.0 and limma 2.7.9)
and found the following issue
when I try to subset a MArrayLM object.
"f" is a MArrayLM object obtained using 'contrasts.fit...and
> class(f)
[1] "MArrayLM"
attr(,"package")
[1] "limma"
> dim(f$contrasts) #lot of contrasts
[1] 8 21
> dim(f$coef)
[1] 109…
div class="preformatted">Dear Yiwen He,
See Sections 8.4 and 8.7 of the limma User's Guide:
http://www.bioconductor.org/packages/release/bioc/vignettes/limma/inst
/doc/usersguide.pdf
I may be able...gt; To: "bioconductor at r-project.org" <bioconductor at="" r-project.org="">
> Subject: [BioC] LIMMA: Help needed for limma analysis with a complex
> design.
>
…
on data analysis of a set of microarray data
exported from
Codelink express 4.1. after reading the limma user guide, i still
dunno
how to read those data with limma, since i only have raw and
normalized
intensity data for each...is a single channel array (Cy5).
i
wonder if someone have experience in handling codelink data with limma
could give me a hand. many thx!
regards,
bert
</div
updated 19.3 years ago • Bert Wong
<div class="preformatted">Hello
I have a questions about correlation of outcomes from Rosetta and
Limma.
I have done Agilent direct hyb's (one condition versus another).
In Rosetta I have splitted ratios without common references and than
have done two sample Ttest.
In Limma I also splitted channels and than fitted linear model. I have
posted design in previous BioC thread with subj "Design…
I have a question on correctly modeling a situtation to find
significantly differentiated genes with Limma. I have Affy arrays for
pediatric patients collected before the patients were treated with a
drug for 4 months. After...patients, I also wish to control for Sex and Age
(continuous variable).
I understand that with Limma I can model the following:
Gene Expression = Age + Sex + Weight Gain
…
div class="preformatted">Hello
I am having some problems with limma again. specifically when using
this for
affy data. This works fine on my laptop and Linux computer but not on
my
colleagues...computer where I have tried to install this for him
His setup is the current limma version 1.3.1 running on R1.8.1 and
Windows
XP. I get:
> contrast.matrix<-makeContrasts(group2-group1,
…
div class="preformatted">Hi,
when I try to install limma, I get the error message below. Can
someone please give me a hint - thanks, Ina
installing *source* package ?limma? ...
** libs
gcc -std...shared -o limma.so normexp.o -L/usr/lib64/R/lib -lR
installing to /usr/local/lib/R/site-library/limma/libs
** R
** inst
** preparing package for lazy loading
Error : unknown namespace directive: fun…
for pre-processing and filtering, then i
take a subset of the normalized group and run this through limma.
I've noticed that if i select my subset differently, the topTable
generated after limma differs. ie rather than select...subset order must be identical to that in the
targets file? Or have I missed something in my current limma code (see
below)?
I believe I'm currently lacking a line which w…
div class="preformatted">* From the authors webpage (http://bioinf.wehi.edu.au/limma/), the
limma
package version is 1.8.22 dated 24 February 2005.
* From the BioConductor (Release 1.5) webpage
http://www.bioconductor.org...repository/release1.5/package/html/limma.h
tml
the limma package version is 1.8.6 dated 27 October 2004.
Is the above discrepancy of nearly 4 months or 15 minor releases
…
div class="preformatted">Dear Ariel,
Thanks for pointing out this problem. In limma 2.7.12 (on
Bioconductor devel now) the design
matrix is no longer subsetted when an MArrayLM is subsetted.
Best wishes...gt; Dear Gordon and BioC users,
>
> I have recently updated R and BioC packages (R.2.3.0 and limma
2.7.9)
> and found the following issue
> when I try to subset…
<div class="preformatted">Hi Bioconductor folks,
I have really been enjoying using the limma package, but I have just
come
across a problem.
When I use the topTable-command, the slot "result$Probe.Set.ID" does
not seem
to match the other entries I am interested in, namely M, P, t.
I am using R 1.8.0, limma 1.5.5 on Affymetrix ATH1-121501 chips.
An example would be:
Output of the topTable-…
div class="preformatted">I use Imagene 4.0 and Limma R package.
My source file are into R directory ... and this is my R shell:
> library(limma)
>
YourSample<-read.table("TargetsSampleTarget.txt
gt; From: Nataliya Yeremenko <eremenko at="" science.uva.nl="">
> Subject: [BioC] Rosetta vs Limma
> To: Bioconductor List <bioconductor at="" stat.math.ethz.ch="">
>
> Hello
> I have a questions about correlation of...a two-sample
t-test using single channel log-ratios. This is a very poor method,
so I'm glad that limma
doesn't give exactly the sam…
div class="preformatted">
Hi, I'm currently using LIMMA to analyze two groups, wt vs treatment
group. LIMMA says gene A is significantly different between the two
groups, p=10E...9.8, 7
if I do >t.test(wt, treatment) I don't get a p-value as low as what is
observed in the limma top table. Why would this happen?
Thanks for the help,
-Kripa
[[alternative HTML version deleted]]…
Hello:
Apart from the original paper that introduced limma-voom, are there any studies that use real data and show that limma-voom works better than limma-trend?
Regards,
Nik Tuzov
updated 7.9 years ago • Nik Tuzov
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
<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">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,
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">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 19.4 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">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 18.4 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
Recent ...
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