sizes (n < 4 per group), it is often better to perform regularization. This can be done using the limma package in Bioconductor._
How this can be done? First, do "regularization" and "normalization" has the same meaning
Order by: Relevance
<div class="preformatted">
>Susan J. Miller sjmiller at email.arizona.edu
>Thu Oct 27 23:14:49 CEST 2005
>
>I am hoping someone can tell me what is causing this problem. I am
>using R 2.1.0, limma 2.0.2 on a Windows 2000 system. I have four .txt
>files containing 2-color microarray data. If I read each individual
txt...<div class="preformatted"…
updated 20.2 years ago • Gordon Smyth
Hi,
I'm performing a differential analysis using limma between control samples and samples from two related diseases from approximately 100 patients in each group. The...Hi,
I'm performing a differential analysis using limma between control samples and samples from two related diseases from approximately 100 patients in each group. The experiment...14 99 100 0
D1 37 2 44 0
…
updated 9.2 years ago • obarton
Dear all,
I have a somewhat fundamental question about differential expression detection in limma. Assume, I want to analyze a micro-array experiment where gene-expression is measured for a limited set of genes (say 1000...Dear all,
I have a somewhat fundamental question about differential expression detection in limma. Assume, I want to analyze a micro-array experiment where gene-expressio…
updated 5.4 years ago • jurgen.claesen
div class="preformatted">
Hi,
Section 11.3 of the limma User's guide introduces the concept of
correlation across technical replicates. To address replicate
correlation
work on other publicly available datasets but the
problem is still the same.
It seems to a bug with Limma or Affy?
Dataset used: http://www.ncbi.nlm.nih.gov/geosuppl/?acc=GSE9711
CODE:
library(affy)
library(limma)
setwd("/home/atul...a script to analyse affymetrix data but its giving an
error
> while using the topTable from limma:
>
> Error in array(x, c(length(x)…
updated 12.8 years ago • Atul Kakrana
You can follow the same construction of the design matrix even though
you
are using limma.
The random approach is a bit more aggressive. For an experiment like
yours, the random approach is explained in Section...8.7 of the limma
User's
Guide:
http://www.bioconductor.org/packages/release/bioc/vignettes/limma/inst
/doc/usersguide.pdf
I would probably...Westergaard <david at="" harsk.dk=""&g…
updated 13.0 years ago • Gordon Smyth
Good evening to everyone!
The limma package (and the related papers) defines the "random effect" in a mixed effect model as a "variable" (e.g. "patient_ID").
However...Then... what is a "random effect"? A whole variable or a coefficient?
In particular, in limma, it's the intercept or the slope (or both) that is free to change according to the block of the mixed effet model?
I got it wr…
replicates of control thesis exceed of 100 times those of treatment condition. The software used, limma, is impaired in DEGs detection despite filtering threshold was set up on the basis of the lowest library size. In particular...limma found up-/down-regulated genes which actually are not (this is clearly showed up by looking at raw counts of such genes
updated 7.7 years ago • baus87
<div class="preformatted">Hello Limma developers and users,
(sorry for the long posting)
Today I encountered a similar problem as the one that was reported by...div class="preformatted">Hello Limma developers and users,
(sorry for the long posting)
Today I encountered a similar problem as the one that was reported...Jason
Skelton.
I'm using Limma version 1.5.7 and R 1.8.1 on Windows…
div class="preformatted">Hello,
I am using limma for 2-color microarray data analysis. I have some
questions regarding MA, design, and contrasts.
1. I have one MA file including
updated 18.3 years ago • Tiandao Li
and I am a PhD student.
I am currently trying to analyse proteomic data from a mass spec using Limma in R. The data contains the normalised abundance values of >1500 proteins across 81 patients. The 81 patients are be...divided into 2 groups: Alive and Dead. I want to use limma to get the p values and fold change for each protein. I have log2 transformed the normalised abundance values a…
div class="preformatted">Dear BioC,
while performing Single Channel Analysis in limma, according to
chapter
9 of the limma users guide, I notice that the R and G foreground
intensities are not correlated at...q+2])) ) + r
+ }
> r
[1] 5069
> # r moet 5069 zijn
> # Separate channel analysis in limma
> MAbetsortedav <- avedups(MAbetsorted, ndups = 3, spacin…
take the average but I am just not
aware of
that. I have used the duplicateCorrelation() function in Limma which
gives
me a -0.04 correlation and its probably because the probes are
position
randomized (even the duplicates...lmFit(ma.quantile, design)
--------------------------------
function: duplicateCorrelation() in limma as follows:
biolrep=c(1,1,2,2)
corfit.avr=duplicateCorrelation(ma.avr.…
updated 16.7 years ago • Vishal Thapar
to an RGList object with 'other'
columns, is a bug. I've committed a fix to Bioconductor in limma
2.16.5
this morning. You should be able to reinstall the new version of
limma in
a couple of days.
Best wishes
Gordon
>...gt; Subject: [BioC] Getting additional columns from Imagene files with
> read.maimages from limma
> To: "bioconductor" <bioconductor at="" stat.ma…
div class="preformatted">
Dear all,
I am trying analyze my 2-color microarray data with limma, and I am
not sure which design I should use. I have total of 4 arrays:array 1
to 4. array 1 and array 2 are from the same biological...at the end, but I am not sure if
this is the best way of doing it.Here's my script :
> library(limma)
> targets <- readTargets("targets.txt")
&…
updated 14.1 years ago • Ella Chang
<div class="preformatted">> Date: Thu, 2 Jun 2005 11:47:15 +0200
> From: Peter S?rensen (HAG) <peter.sorensen2@agrsci.dk>
> Subject: [BioC] random block effect and technical replicates within
> array at the same in linear model using Limma ?
> To: <bioconductor@stat.math.ethz.ch>
>
> Dear list,
>
> I hav…
<div class="preformatted">Hello,
I was wondering if there was any (easy) way to handle a nested design
in
limma. I looked in the Bioconductor archives, but the only references
to
nested designs weren't really nested - one was just a...<div class="preformatted">Hello,
I was wondering if there was any (easy) way to handle a nested design
in
limma. I looked in the Bioconductor archives…
updated 19.9 years ago • Jenny Drnevich
Dear Bioconductors,
This may be more a question of statistics understanding but it is related to Limma.
Is it possible to perform an Anova using functions from the Limma package? If so, how can a post hoc test be applied to the...design I have array data, different clients, time course, stage of disease and treatment. The Limma manual eludes to Limma being equivalent to Anova in some cases for …
updated 11.2 years ago • john herbert
<div class="preformatted">Hello List,
I am just forwarding Lorenzo's response to the list as he forgot to
copy the
list. May be, this is of use in the future.
I think, your design is a unbalanced randomized incomplete block
design, so
it doesn't matter if you have one treatment or multiple for a single
block.
Also, the duplicateCorrelation is estimated from the data and the
estimate
(0.131…
updated 15.2 years ago • Sunny Srivastava
and the most of the
genes are the same in both sets). I am not sure how can I deal with
them using Limma.
I assume that it is not possible to perform a global print-tip loess
normalization, so, Could be it possible to normalize
the following
comparisons: 1-2, 2-3, 3-4, 4-5, 5-6 and 6-1?
I know there is some information about Limma and time course
experiments
but that example uses one-color arrays so I'm confused about how to
apply
that to my experimental
<div class="preformatted">Hi,
I am doing an analysis of a colleague's dataset, but I have troubles
reproducing the results on fold changes he obtained by manually
calculating these in Excel.
The design of the experiment is as follows:
- affymetrix arrays, RMA normalized
- subjects got 3 treatments (T1, T2, T3), for now we focus on the
differentially expressed genes between T2 and T1.
- si…
2009 10:03:45 +0200
> From: Benoit <benoit.loup at="" jouy.inra.fr="">
> Subject: Re: [BioC] Limma lmFit function and spot quality weights
> To: Bioconductor mailing list <bioconductor at="" stat.math.ethz.ch="">
>
>...gt; robust differential expressed genes.
> Concerning the weights, I am a very new user in R and Limma and it's
not
> ea…
updated 16.4 years ago • Gordon Smyth
each individual.
I have used this code so far.
<pre>
library(ArrayExpress)
library(limma)
rawdata=ArrayExpress("E-blablabla")
eset<-rma(rawdata)
Patients<-factor(rep(1:5,2))
Tissues<-factor(c(rep("V",5),rep("A",5)))
design...Patients+Tissues)
fit<-lmFit(eset,design)
fit<-eBayes(fit)
</pre>
According to limma User's Gu…
div class="preformatted">Hi
I'm going to be teaching use of limma to a bunch of non-statisticians
later this month, and I wondered if there were any slides or other
resources that I could
is expected and needs to be preserved) >combine normalized samples back into one data table > limma DE analysis using one single factor matrix design (please see codes below). I then plotted log2FC of toptable output...lt;- gsub("groups", "", colnames(design))
rownames(design) <- colnames(limma_df)
fitall <- limma::lmFit(limma_df, design)
meanint <- apply…
updated 2.3 years ago • Erin Yu
for this design (or a design similar to this one), but there
is
apparently no (easy) solution in limma, I was wondering if anyone
could
suggest a package for differential expression analysis that allows
dealing with...gt; Hi Naomi and list,
>
> some time ago I asked a question on how to model an experiment in
limma.
> I think I need some additional help with it as the experim…
updated 16.7 years ago • Paolo Innocenti
27 Jul 2009 13:41:06 +0200
> From: Benoit <benoit.loup at="" jouy.inra.fr="">
> Subject: [BioC] Limma lmFit function and spot quality weights
> To: bioconductor at stat.math.ethz.ch
>
> Hello,
> I'm using Limma to assess...in a
> classical design experiment "Two Groups: Common Reference" as
describe
> in the Limma documentation.
&g…
updated 16.4 years ago • Gordon Smyth
0 at the bottom left of the image.
Can I get rid of this? Have I missed something obvious in the limma
user
guide or the help page? I appreciate I am not using vennDiagram for
its
original purpose and as such this might not...be possible, if not is
there
another way around it?
Code:
library(limma)
set1 = scan("set1.txt",what='character',sep="\n")
set2 = scan("set2.txt",what='character',sep="…
updated 17.5 years ago • james perkins
What was the very first paper to describe "limma-trend"? By "limma-trend" I mean the one described in Law (2014), but I am not sure that was the first time.
Thanks,
Nik
updated 10.3 years ago • Nik Tuzov
div class="preformatted">Dear List,
I have been working with LIMMA and I'm a bit confused by the
linear
models. I have a group with 4 factors. I want to remove covariates
from the main effects
I am trying to find a way to identify differentially
expressed genes; I was recommended to use limma. I read in the manual
that I can use data analysed with other packages (like affy and
others)
or that I can import data from
div class="preformatted">Dear Bioconductor,
In limma package, contrasts.fit() function is very useful. I am
wondering whether there is a similar function for lme object.
Thanks
Hello,
I recently completed running limma-trend to find differentially expressed genes influenced by the sex, tissue type, and infection status of a plant. For...example, one comparison was male infected flowers to female infected flowers. According to limma, there are significant differences in many of my comparisons, but in trying to get the output data, I'm unable to obtain...with the log2FC …
```
# DGE Analysis with Limma.
# Model matrix.
design <- model.matrix(~0+PHENO$Group)
fit <- lmFit(VAR.exprs, design)
contrasts <- makeContrasts(G3- G1, G3...DGE Analysis with Limma.
# Model matrix.
design <- model.matrix(~0+PHENO$Group)
fit <- lmFit(VAR.exprs, design)
contrasts <- makeContrasts(G3- G1
updated 22 months ago • Amit
Dear all,
I am struggling with using limma in the case of many missing values.
Here is a small example:
```
df = data.frame(
g1=c(5,5,6,6,NA,NA),
g2=c(5,5,NA,NA,6,6),
g3=c(NA,NA,5,5,6,6),
treat...5.5 -0.5 NA
g3 5.5 NA -0.5
```
Is it appropriate to use limma in such scenarios? Did I something
wrong
or misinterpreted the results? I thi…
updated 17.8 years ago • Hans-Ulrich Klein
When trying to adjust data for batch effects using the respective limma (v3.34.9) function removeBatchEffect() I got strange values (at least to my understanding).
My question: In the example...When trying to adjust data for batch effects using the respective limma (v3.34.9) function removeBatchEffect() I got strange values (at least to my understanding).
My question: In the example below would…
updated 7.5 years ago • jf1
gt; To: bioconductor at r-project.org
> Subject: [BioC] mergeScans function in limma - minFactor error
> Message-ID: <4F211E29.2000407 at ibch.poznan.pl>
> Content-Type: text/plain; charset=UTF-8; format...flowed
>
> Hello everyone.
>
> I am using limma for microarray analysis for some time. Now I am
trying
> to use mergeScans …
updated 13.9 years ago • Gordon Smyth
div class="preformatted">I tried the command to read my .txt file into R for limma analysis,
but I got
the following error message:
Error in file(con, "r") : unable to open connection
In addition: Warning message...try
>
>?read.maimages
>
>or
>
>help.start()
>
>and take the 'Packages', 'limma' and '3.ReadingData' links.
>Best wish…
<div class="preformatted">Dear Augusto,
It's fixed in Bioconductor developmental version, see
https://www.stat.math.ethz.ch/pipermail/bioconductor/2008-July/023363.
html
Best wishes
Gordon
> Date: Fri, 15 Aug 2008 18:18:08 +0100
> From: Augusto Rendon <rendon at="" ebi.ac.uk="">
> Subject: [BioC] Error with normexp in limma background correction
> To: b…
Yang and Thorne, 2003).
However,
I do not understand how these approaches are applied in the limma
package
(Bioconductor). For two channel normalization you use a within array
and
between array normalization and for...in Smyth and Speed (2003) that scale normalization between arrays is
recommended. Which function in limma does this calculation? is it the
normalizeBetweenArrays (method= scale)?
3…
updated 13.5 years ago • Maite Iriondo
<div class="preformatted">
>Date: Tue, 16 Aug 2005 18:01:40 -0300
>From: Marcelo Luiz de Laia <mlaia at="" fcav.unesp.br="">
>Subject: [BioC] heatmap and hcluster from limma out put object
>To: bioconductor <bioconductor at="" stat.math.ethz.ch="">
>
>Hi Bioconductor's Users,
>
>I found in the...Marcelo Luiz de Laia <mla…
used the Affy package to read in the CEL file data and GCRMA to normalize. Finally I used limma to analyze (lmFit and eBayes). Now the FC coefficients I get back from limma appear to be log2(2^(mean(test ...So now we have -14.4 fold downregulation.
The example given is of course an extreme, but using the limma method there ar…
<div class="preformatted">> Date: Tue, 20 Dec 2005 21:12:24 -0500
> From: Naomi Altman <naomi at="" stat.psu.edu="">
> Subject: [BioC] Limma Coefficients using lmscFit
> To: bioconductor at stat.math.ethz.ch
> Cc: QING ZHANG <qxz5 at="" psu.edu="">
>
> Being a big...20 Dec 2005 21:12:24 -0500
> From: Naomi Altman <naomi …
<div class="preformatted">Dear BioC-list
I have data from a microarray experiment comparing 12 different growth
conditions for bacteria.
This are the conditions
BC7ppm BC9ppm CH3COOH EtBr EtOH Glycerol gr15 gr46 HCl NaCl NaOH PK
PK is the normal condition and it is of interest to find genes that
are differentially expressed in PK and the other conditions. The
experiment is a reference de…
updated 20.9 years ago • Ingunn Berget
Hi, I'm a beginner in LIMMA analysis and also microarray data.
Hope someone can give me some suggestions.
Here is the frame of my microarray data...I think my data frame is similar to **9.7 Multi-level Experiments (p.50)** in the user guide of LIMMA. (https://bioconductor.org/packages/release/bioc/html/limma.html)
Is it correct?
Then I modified the code in the user guide...adjust="fdr…
updated 3.7 years ago • Wendy
This is a question which came up recently regarding the RNA-Seq in limma/voom, and limma/voom using the variancePartition function `dream()`.
When following the workflow outlined in this document...release/bioc/vignettes/variancePartition/inst/doc/dream.html)) we can see at the beginning a limma/voom analysis resulting in an object called `vobj`. This object was created by passing the DGEList …
updated 6.3 years ago • Ben
2005 18:30:13 -0500
> From: Pita <pwilkinson_m@xbioinformatics.org>
> Subject: [BioC] Using limma with contrast matrix ,replicate spots,
> To: bioconductor <bioconductor@stat.math.ethz.ch>
>
> What is the significance
<div class="preformatted">Christine,
On Tue, 23 Sep 2003 c.chaffer@pgrad.unimelb.edu.au wrote:
> Hi James,
>
> How's it going? I have a question for you!!
>
> I've been playing with my data in Limma and am wondering if there is
a way
> to get a list of the genes that are represented in the intersection
of the
> venn diagram...gt;
> H…
updated 22.3 years ago • James Wettenhall
anova, but I’d like to take advantage of the more sophisticated and task-appropriate models in limma.
I’m generally getting my data from GEO. Consider the [expression of estrogen receptor beta](http://www.ncbi.nlm.nih.gov...SHH
4.383280 5.117186
How can I get to a similar point with limma? When I’ve used limma up to this point, I’ve started wi…
updated 10.4 years ago • mamillerpa
div class="preformatted">Dear Gordon and Bioconductor list members,
I am using limma to analyse an unlinked two-colour array experiment
consisting of 31 arrays (with 34,992 spots on each array) and 38
unique...separate channel analysis using the function lmscFit() and tried to
follow the example given in the limma user's guide (see below) but
found that the "intraspotCorrelation()" gives me n…
Hello all,
I have a few questions about the linear model in limma.
I am doing limma/voom on my expression results, looking for differences between treatment1 and treatment2. I have several...Hello all,
I have a few questions about the linear model in limma.
I am doing limma/voom on my expression results, looking for differences between treatment1 and treatment2. I have several batches, so my …
updated 8.9 years ago • jalali4
the cancer gene expression data from TCGA repository as the input data of CAMERA function in package 'limma'. however, i have some confusion about the data preprocessing.
I downloaded normalized data and process it using
Hello!
I am using limma with the voomWithQualityWeights functionality and have had no problems with any errors. I was really just wondering
div class="preformatted">
Hi,
I tried to use limma two-sample experiment. I got error when doing
lm.series.
below is the scripts of what happened. Could somebody tell me
<div class="preformatted">Hi everyone,
I'm trying to test the effect of different medical parameters (fators)
on my
data with limma but I get a troncated design matrix.
I've two factors 'UNOS' and 'Etiology' (with 3 and 2 levels
respectively)
listed below:
Target.txt...Hi everyone,
I'm trying to test the effect of different medical parameters (fators)
on my
data with limma but I get a tr…
preformatted">I have a 2 x 3 factorial cDNA microarray experiment which I would like
to analyse in Limma. I need, however, some advise on the constuction
of design and contrast matrices - which is not straightforward to
understand
updated 21.8 years ago • Per Gregersen
div class="preformatted">Hi list,
I am trying to call makeContrasts() in limma to accept character
vector
of all samples vs control. But it seems that makeContrasts() consider
only the first element
I noticed that there is inconsistency between the t and p.value on the
topTable output using Limma package to analyze a dye swap two channel
array
experiment.
logFC AveExpr t P.Value adj.P.Val B
1401 3.216254 11.74137
Recent ...
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