div class="preformatted">Hi all,
I'm performing an analyis in limma with 3 groups. Normally I would set
up a simple analysis with 3 contrasts:
groups <- factor(c(A,A,A,B,B,B,C,C,C))
design <- model.matrix
Order by: Relevance
div class="preformatted">Dear List Members,
in limma manual is stated that
"A zero weight indicates that the spot should be ignored in all
analysis as
being unreliable".
lmFit
this may be a simple question. I
have a
problem sometimes when using the plotDensities function in Limma, in
some
cases the plot produced is on such a scale that the lines are not
distinguishable. Usually the intensity axis
For a dataset I'm working on, we would like to use the limma package for differential expression analysis. We are using `limma::removeBatchEffect` (doing it for downstream analysis...before using limma for differential expression analysis. Would it be okay to still include the batch covariate in the model to account
updated 6.8 years ago • jmoon1194
An ordinal variable is just a special case of a categorical variable,
and
you include it in the limma design matrix just as you would any other
categorical variable. For example:
DiseaseState <- ordered(DiseaseState...scott.robinson at glasgow.ac.uk
> Subject: [BioC] Can I input ordinal variables into a model in Limma?
>
>
> I am working on some microarray …
updated 12.3 years ago • Gordon Smyth
div class="preformatted">I'm using limma and have set a spot types colors to "indigo". When I
then run plotMA(RG[,1]) I get the following message: "Error in
plot.xy(xy.coords
div class="preformatted">Hi all,
I am using the lmFit function in limma, and am trying to extract the
standard deviation of the fitted values. I know that "fitted" exists
to
extract the fitted
<div class="preformatted">I tried this approach, but I believe that the problem is that spots
that are
adjacent on the array are expected to have higher correlation than
spots
that are in the upper and lower half of the array for instance. This
means
that duplicates that are lets say 10 spots apart probably are more
correlated than those 200 spots apart, and I am afraid may "disturb"
the
a…
div class="preformatted">Dear Bioc Users,
I'm using the limma library for differential gene expression analysis.
I
have a question about how to choose the p-value.
These are my contrasts
Mut2
Mut3
Mut1+2
Mut1+3
I want to run a differential analysis per time point using limma, using the WT as a control in each respective time point.
My design matrix is specified by
design <- model.matrix(~ 0 + fac...Mut1_1h, Mut1_2h, ... , Mut1+3_24h, Mut1+3_48h)
Would there be any difference between using limma/voom with time series and the Time course section in l…
updated 3.7 years ago • rina
overall anova (4 groups; is there any difference across groups) using the following design matrix in limma
<pre>
(Intercept) B C D
1 1 0 0 0
2 1 0 0 0
3 1 0 0 0
4 1 0 0 0
5 1 0 0 0
6 1 0 0 0</pre>
I have used ROAST (in limma) in the past with a specific contrast...design_matrix,contrast=10,nrot=3000).</pre>
…
updated 11.2 years ago • Juliet Hannah
div class="preformatted">Dear all,
I am encountering the following error with read.maimages in limma
package.
Error in dimnames(x) <- dn :
length of 'dimnames' [2] not equal to array extent
Following are some details:
Here is the...searched the web for solutions but couldn't find any. Some of the
suggestions I found was to update limma version. However, in my case,
I had
re-installed…
updated 14.8 years ago • Hari Easwaran
<div class="preformatted">
Dear all,
I am trying to create a customized cut flow with the affy/limma
packages. In order to assign different cut-off values between
different arrays would be to first make one cut-off and then use the
remaining expression set in further analysis. When working with the
affy/limma packages, I read and normalize my data with the justRMA()
function, fit a linear m…
updated 13.9 years ago • Guest User
distribution of p-values for a treated-untreated comparison
(3 reps) after the eBayes procedure in Limma?
Expressed in my usual 'comprehensive' style ;-)
Following on from a previous thread I've started to look more into the
p.value...index.html
Has anyone done similar? And is this approach valid using the eBayes
moderated stats of limma?
This approach 'appears' ok if you have alot of replicat…
that we tried
and
the problems we faced. We searched the archives without much success.
library(limma) # version 2.3.3
dd <- model.matrix( ~ disease + gender + batch, cl )
head( dd )
(Intercept) diseasenormal gendermale batchtwo batchthree...0),
Batch2minus1=c(0,0,0,0,1),
Batch3minus2=c(0,0,0,-1,1) )
2) From reading the LIMMA user guide, we think decideTest…
where I make simple
comparisons between a control and a treatment group. I used vsn to
normalize and limma to find differentially expressed genes. I used
"topTable" with number=Inf and p.value=0.05 to get all significant
genes...the
same I used for my own analysis. Thanks in advance!
Eva
library(ALL)
data(ALL)
library(limma)
f = ALL$mol.biol
mat = model.matrix(~f, ALL)
lm = lmFit(ALL, mat)
…
updated 15.1 years ago • Eva Benito Garagorri
Is it possible to run limma on an ESET containing the data of 4 normalized datasets that have been merged? If yes please advise. I am trying to use...Is it possible to run limma on an ESET containing the data of 4 normalized datasets that have been merged? If yes please advise. I am trying to use the
updated 10.5 years ago • Vani
I used the current command in Limma to create volcanoplot, the Y axis is "LogOdds" and X axis is "Log2FoldChange".
I would like to have Y axis as "log10Pvalue". how
updated 9.7 years ago • mheydarpour
div class="preformatted"> From R 2.6.0 onwards it's my intention to maintain the limma package
only on Bioconductor, and not also on CRAN, as has been done for the
past few years. If this causes anyone any serious
between
Tumors and normals.
In such cases how can I create model.matrix
Following is taken from Limma manual:
design <- model.matrix(~ -1 +
factor(c(1,1,1,2,2,3,3,3)))
my question:
1. what is '~ -1' is for?
2. Will this work for my study structure
<div class="preformatted">In the old limma, one could subset a MAlist or RGlist (let's say
RGnorm
is a MAlist) by entering:
RGnorm[,1:3] for the first three columns for example...div class="preformatted">In the old limma, one could subset a MAlist or RGlist (let's say
RGnorm
is a MAlist) by entering:
RGnorm[,1:3] for the first three columns for
expressed vs not-detectably-expressed in my tissues
of interest.
I have a loop design, and am using limma to identify differentially
expressed genes. Is it possible to use limma to also do the analysis
I suggested above? I assume...that this would involve using the
separate channel functions of limma, but am unclear on how to
approach it.
Many thanks,
John
--
John Fowler …
Hi bioC community,
Until now I used comBat to remove the batch effects present on my datasets.
After reading the article "Methods that remove batch effects while retaining group differences may lead to exaggerated confidence in downstream analyses" <http://biostatistics.oxfordjournals.org/content/early/2015/08/31/biostatistics.kxv027.full.pdf>, I decided to block for batch effect in limma…
updated 10.3 years ago • eleonoregravier
for a qPCR array with 96 genes. I was wondering if someone knows about a couple of papers where limma is used to assess DEGs in a qPCR array and not on another microarray platform or RNA seq. I know it's perfectly possible...a really hard time finding the aforementioned literature. All I've found so far are works where limma is used upon another technology and the qPCR is only used to confirm DEG…
updated 7.4 years ago • Daniel Moreno
2005 16:52:34 +0200
>From: "Groot, Philip de" <philip.degroot at="" wur.nl="">
>Subject: [BioC] Limma: how to calculate ordinary p-values omitting
the
> eBayes() command
>To: <bioconductor at="" stat.math.ethz.ch="">
>
>Hello...Gordon Smith helpen me a while ago with calculating regularised
p-values
>(paired t-test) using Limma.…
div class="preformatted">Dear BioC,
I'm getting an error using the lmFit function within limma. I'm using
R
2.4.0 with limma version 2.9.1.
A little background about the experiment:
I use two color agilent arrays containing
div class="preformatted">Dear David,
You have two choices of how to do this in limma. You can either add
the
gene symbols (and GO category or anything else) into the fit object,
or
alternatively you can add...gt; To: "bioconductor at r-project.org" <bioconductor at="" r-project.org="">
> Subject: [BioC] limma topTable annotation
>
> Hi Folks,
>
> As a…
I get totally different results.
The only difference between the two runs lies in updates to R and
limma in
the meantime. Unfortunately, I did not record which version of R,
limma etc. I
had used, originally. My current environment...lt;- eBayes(fit)
tt <- topTable(fit, number=100)
I have siftet through the changelog of limma hoping to find a hint
about
some changed default or be…
updated 17.5 years ago • Philipp Pagel
div class="preformatted">Dear Sally,
The limma output shows that it has read all your ImaGene files
correctly. I suspect that your targets file has a spurious blank...line
at the end of the file that you need to remove. This causes limma to
try to read a non-existent file with name "".
Best wishes
Gordon
>Date: Thu, 03 Jan 2008 11:33:24 -0800
>From: Sally <sagoldes...at="" …
I have several questions about analyzing miRNA sequencing data using limma voom. Most of these questions relate to the fact that the composition/distribution of miRNA sequencing data is very...type. Furthermore, just a few of these miRNAs can account for up to 50% of the miRNAs expressed. Can limma voom still be used for differential expression of miRNAs between two different cell types when the …
Hi,
Recently, I'm doing DE analysis on some RNA-seq materials. We have both raw count data matrix and also TPM data of all samples. At first, We performed DE analysis on DEseq2 using the raw count data, and we got some results. Then, to make sure the signals we found is correct . We also tried to run Limma by using its TPM data. (The TPM and raw Count data are coming from the same group of sam…
<div class="preformatted">Dear Maxim,
Thanks for the code example. Your design matrix really is singular,
as
can easily be confirmed in a variety of ways. This is not a bug in
limma.
Also this not an "error". It is a perfectly helpful diagnostic
message
that the software is giving you.
Best wishes
Gordon
> Date: Wed, 17 Mar 2010 16:11:10 +0000
> From: "Freydin, Maxim" &…
if anyone here knows something about the software, and if this
software has more function than limma.
Thank you very much!
--
Xiaopeng ZHANG<xpzhang@genetics.ac.cn></xpzhang@genetics.ac.cn></div
div class="preformatted">Hi,
I am a complete beginner to Linear Models and using the LIMMA package.
First I have a general question as to what are good intro texts
explaining Linear Models in general.
I also have
div class="preformatted">Hi!
I am analyzing custom two color agilent array by using limma package
and
I am having some problems with the read.maimages
comand:
I launch this comand:
> read.maimages("Targets
<div class="preformatted">Hi All
I haven't used LIMMA for a while, but I remember that when I did
there was a special way to handle duplicate spots. However the
layout of the array...div class="preformatted">Hi All
I haven't used LIMMA for a while, but I remember that when I did
there was a special way to handle duplicate spots. However the
layout of the
List,
In an earlier posting, Gordon Smyth recommended
a tentative cutoff of B>=0 for Limma output.
Is it okay to publish Venn diagrams based on this
cutoff or should the cutoff be validated by spot-checking with
summarized, normalized, background corrected data. You
can then feed the eset object directly into limma, without writing it
to
disk. You first need a design matrix. I will make assumptions here
about
the structure of your data...You can now output in text files, HTML tables, whatever
you like. You should certainly peruse the limma User's Guide to get
more
detailed information, and you should als…
updated 12.3 years ago • James W. MacDonald
div class="preformatted">Hello everybody
After successful importing the data to the LIMMA,
I followed all steps and finally obtained "topTable".
(the data were 44K Agilent)
I'm surprised that my data set doesn't have
updated 20.2 years ago • Nataliya Yeremenko
Jenny, Gordon, and the list,
This is a follow-up on the thread about handling nested design using
LIMMA posted last year (please see
https://stat.ethz.ch/pipermail/bioconductor/2006-February/012018.html
).
I have a data set...they are usually
highly correlated) to get one measurement for each biological samples,
then fitted LIMMA with a nested design model matrix (see below).
Is this OK and li…
Moghaddasi <a.moghaddasi at="" gmail.com="">
>Subject: [BioC] automating makeContrasts call in limma
>To: bioconductor at stat.math.ethz.ch
>
>Hi list,
>
>I am trying to call makeContrasts() in limma to accept character
div class="preformatted">
Thank you in advance for answering my question about limma package!
The function read.ilmn() reads in probe_file.txt and
control_probe_file.txt seperately for illumina microarray...Expression BeadChip data look like below? How can
I use read.ilmn and follow the steps described in limma user guide
15.3?
It is just one file containing the columns:
TargetID ProbeID sam…
updated 12.6 years ago • Guest User
Dear BioC's,
I'd very much appreciate input on my design to achieve a sound
analysis
with limma.
Initially i thought i could get away with a two-factor design:
-treatments, 'S', 'E' & 'L'
-tissues, 'R' & 'C'
(targets file at bottom...focus on another aspect of this
experiment(*fyi see at bottom). What i'm trying to acheive now with
limma is not concerned with 'time', merely id…
Hi all. Currently I am working on differential gene expression analysis using limma R package. The metadata of my dataset includes both Treatment and Time variables. Example of the same is shown below...Hi all. Currently I am working on differential gene expression analysis using limma R package. The metadata of my dataset includes both Treatment and Time variables. Example of the same is shown b…
updated 3.8 years ago • bageerathan.v
gt; Para: Christian Probst
> Cc: BioC Mailing List
> Assunto: [BioC] Genechip experiment in limma
>
> At 02:48 AM 22/08/2003, Christian Probst wrote:
>>Gordon,
>>
>>I succeed in loading the cDNA microarray data...As I need a spatial
>> normalization, I will try to do it before the use of limma package.
>
&a…
updated 22.4 years ago • Gordon Smyth
basic for the list, but I've had a few people
contact me who struggle to read in OGT arrays using limma. The code
below works. If anyone has any trouble, feel free to contact me.
Mick
# where files is a list of filenames
library...limma)
RG <- read.maimages(files = files, source = "generic", columns =
list(R="rMeanSignal", Rb="rBGMedianSignal", G="gMeanSignal",
Gb="gBGMedianSignal
updated 17.1 years ago • michael watson IAH-C
<div class="preformatted">> Dear all,
>
> I would like to use Limma to read in not only the signal and
background
> value, but also to read in additional spot data (spot quality flags,
in
>...div class="preformatted">> Dear all,
>
> I would like to use Limma to read in not only the signal and
background
> value, but also to re…
dataset we are analyzing, and I have a general question about the
quantile normalization options in Limma.
Our dataset shows a relatively pronounced batch effect, so the
between-array normalization is a critical step. We have...normalizeBetweenArrays(MA.Loess$M,
method="quantile")
Because this is not one of the built-in Limma functions, I was
wondering whether there any obvious reason why this …
updated 14.6 years ago • Wlasiuk Battagliotti, Gabriela - wlasiuk
array) experiment.
>
>After spending a while knocking my data into shape for analysis by
>"limma" (or so I thought) I calculated the top 30 regulated genes
>for a couple of experiments and noticed the same gene appearing...2003, Jason Skelton wrote:
> > >On a different note
> > >The arrays I have tested LIMMA on have 2 duplicat…
<div class="preformatted">Hello,
I have a question about which analysis to do in LIMMA. I did three
experiments (three biological replicates) each with one treatment
microcosm ("L") and one control microcosm ("D"). For each experiment,
I sampled both the treatment and control microcosms at 5 time points
(0 hr, 2 hr, 6 hr, 12 hr, 24 hr). With 3 replicate experiments * (1
treatment + 1 contro…
Dear all,
I am quite new to limma and need to ask how to export the normalized data. I want to use them in graphical data exploration and presenatation...So, I do something like this (following the Mattick Lab post):
<pre>
library(limma)
targets <- readTargets('targets.txt')
x <- read.maimages(targets, path = 'mydirectory', source = 'agilent', green.only =T)
y &…
Could someone suggest for me a text explaining in details the mathematics behind LIMMA when we have a quantitative outcome. Most of the available literature I have come across explain LIMMA mathematically
updated 9.1 years ago • Linda Chaba
Hello,
The limma user's guide states that:
> The linear model and differential expression functions are applicable
> to data from...Hello,
The limma user's guide states that:
> The linear model and differential expression functions are applicable
> to data from any...I have a more complex study design that would benefit from the statistical modelling capabilities o…
<div class="preformatted">Dear limma users and developers,
At our laboratory we analyze our MA data using limma. Currently we
have
created a dedicated array on which the same set of genes is spotted
three
times on one slide. Actually it is one design spotted three times. In
Imagene you can now create a META gid for (in this case) the 4*4
grids. This
grid you call grid A.. Then you can copy…
of alison
waller
Sent: Fri 30/11/2007 9:13 PM
To: bioconductor at stat.math.ethz.ch
Subject: [BioC] Limma - error reading in .gpr files
Hi all,
I'm having a problem reading in my genepix files using read.maimages.
If
anyone could...a location in the spreadsheet where
there
might be a problem.
Thanks so much,
alison
> library(limma)
> targets<-readTargets("VCMeOHTargets.…
<div class="preformatted">
Hi all,
Firstly thanks for all the help in the past!
Now, I have biological replicate arrays for which different amounts of
RNA have been used (3 micrograms and 4 micrograms). So a fairly big
difference of over 30%.
I am performing normalizeWithinArrays and then normalizeBetweenArrays
in
limma. The between array normalization is necessary since the arrays
were …
updated 21.6 years ago • Helen Cattan
04:31 -0400
> From: "Lance E. Palmer" <lance.palmer at="" stonybrook.edu="">
> Subject: [BioC] LIMMA P-value calculations/Suggestions for flagged
> data
> To: bioconductor at stat.math.ethz.ch
>
> I just had a question...concern about P value calculations in Limma (I
am
> using latest version of Bioconductor)
>
> I recentl…
I've had several requests for references to published papers in the
biology
literature using the limma package. There have been three articles
appear
since June that I know of:
Golden, T., R., and Melov, S. (2004). Microarray analysis
updated 21.4 years ago • Gordon Smyth
div class="preformatted">Dear all,
I am using limma for the analysis of a factorial experiment for the
first time.
I would greatly appreciate your help re to few questions
Recent ...
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