mail, I have
four arrays in a replicated dye swap experiment. After carrying out
the
analysis in limma, I find that 360 out of 4600 genes have an
unadjusted
p-value <= 0.05. However, when I adjust these using adjust="fdr", all
of
Order by: Relevance
Dear list,
I have a simple doubt concerning how I should deal with the *replicate
day*
effect using limma.
It is clear that I have a *day effect* in my data that it has to be
taken
into account in the model. I am using 2 different model
div class="preformatted">Dear Bioconductor users,
I just began to use limma package for the analysis of microarray data.
I
want to include in the analysis two factors (treatment and time) and
the
updated 11.9 years ago • David Moriña Soler
<div class="preformatted">Hi, I have been given a bunch of data; some of it is from a 384x164
chip and another
that is 532x85.
First question, how can I read these in and normalize them together?
I can create separate target files for each set. But then how to
merge?
I have seen the limma section title 'Combine RGList, MAList, EList or
EListRaw Objects',
but since there are different rows …
<div class="preformatted">Yi:
Could you send the output of sessionInfo() to the list? I am attaching
mine at the end.
I guess that you are using an old version of limma (when field
dimensions
had only one block). It is recommended to upgrade to a more recent
version
(e.g., 2.10.5).
> so read.imagene() calculates the total number of spots as prod(FD):
> nspots <- prod…
I have run an anova on this gene and with a bit of fiddling I can
derive all the figures supplied by limma in both approaches and how
they are linked. Except for when they should be 4 times bigger or 4
times smaller.
Regards
John...usadel@mpimp-golm.mpg.de]
Sent: 24 February 2009 12:18
To: john seers (IFR)
Subject: Re: [BioC] limma - interpreting factorial design
Dear John,
could you please a…
div class="preformatted">hi,
i am using limma to analyze agilent chip data with four groups of cell
lines: wt, mut, wt+S(stimulated), mut+S.
goals: 1)find genes difference
incorrectly), but the
background channel are not swapped. What gives? Does the latest
version of limma know how to read Genepix v. 3 (as opposed to version
5/6, which have different column orderings).
Thanks,
G</div
1) I am new to limma and to R
2) I would like to subtract the mean background from each sample individually. I don't know how to do this...with limma and maintain the same object class.
3) I can export the RGlist to a spreadsheet and do this manually pretty easily...I think, but how can I import the file back into limma and keep the same object class?
Thank you
&…
updated 10.4 years ago • jjotto
per time point) based on a common reference
(=pool of all the conditions) design dataset with the limma package.
By reading the contents of the limma user's guide, I found limma very
interesting to first pre-process the data...script I'm have been using so far in order to normalize
the data within and between arrays.
library(limma)
targets=readTargets("targets.txt")
RG=read.maimages(files=c("1 R…
I’m transforming the abundance matrix log2 counts, performing quantile normalization, then running a limma pipeline with eBayes(trend=TRUE, robust=TRUE). Putting the code at the end of the post.
Questions:
1. Are there additional...total ion chromatogram plots and I’m figuring out what to do.
3. Thoughts on using [POMA][3] vs limma? I’m most familiar with limma/voom and wanted to ask fir…
updated 2.9 years ago • wiscoyogi
<div class="preformatted">
> Date: Wed, 14 Mar 2007 10:19:32 -0800 (PST)
> From: "Sergio Barberan" <barberan at="" biology.ucsc.edu="">
> Subject: [BioC] Limma time course with two-color microarrays
> To: bioconductor at stat.math.ethz.ch
>
> Dear list,
>
> It might be a really easy problem but I can not figure out how to do
it.
…
<div class="preformatted">Dear Elmer,
This seems to be a locale problem. I don't know much about locale
problems, but my understanding is that they arise from using an
extended
ascii character which is understood in one language, but not supported
by
the software you're using. My guess is that your Windows R is
compiled
for a Spanish locale whereas your Unix version is compiled for US
En…
yong.li at="" zbsa.uni-freiburg.de="">
> To: bioconductor at r-project.org
> Subject: [BioC] limma design problem with a two color dataset
>
> Dear list,
>
> I am analyzing a two color microarray dataset using limma...normalization have been
done
> but I was not able to make a design matrix. I have read the whole
limma
> users guide, espe…
updated 14.8 years ago • Gordon Smyth
Dear Sarah,
A problem with your code is that you are trying to read a comma-
separated file whereas limma
assumes that files are tab-delimited. To read a csv file, you need to
specify sep="," in the
read.maimages call.
If your problem...Tue, 1 May 2007 13:55:55 -0500 (CDT)
> From: sltucker at artsci.wustl.edu
> Subject: Re: [BioC] limma read.maimages for scanarray express .csv
&a…
div class="preformatted">Hello,
I am using Limma (version 3.12.0) to read 2-channel dye-swap files
from an Agilent image analysis scanner, where each sample has 2
files...one for cy3 and one for cy5.
However, the only reference to such a 2-file input in the limma user
guide is to "ImaGene".
When I try to read the files and the target file using the following
commands:
RG = read.maimages
<div class="preformatted">Dear list,
I am analysing some microarrays with the limma package, and so far
have
discovered no significant DEGs. I'm unsure if this is because there
really are no DEGs or I've misunderstood the limma package. I'm
hoping
someone with more experience can tell me if my analysis is correct,
or,
if not, where I've gone wrong.
I have...div class="preformatted">D…
div class="preformatted">I am new to Limma and have some basic questions to ask about the
matrix
design:
(1) I have used RNA-Seq methods to get gene expression profiles...2) For each patient, we got expresson data of the normal tissues and
cancer tissues.
I want to use Limma to analyze these RNA-Seq data and want to address
the
following questions:
(1) Differentially expressed genes in Norm…
into limma using the
instructions in the limma User's Guide starting page 14 "What should
you
do if your image analysis program is...I
demonstrate this below.
Your emails suggest that you have not yet read any two-color data into
limma. It is essential that you try some simple examples before
trying a
large dataset from ArrayExpress, which will have...me, but I doubt that you are interpretting …
updated 17.2 years ago • Gordon Smyth
11:56:17 +0100
> From: Hans-Ulrich Klein <h.klein at="" uni-muenster.de="">
> Subject: [BioC] limma - different parametrization and weights
> To: Bioconductor list <bioconductor at="" stat.math.ethz.ch="">
> Message-ID...gt; Content-Type: text/plain; charset=ISO-8859-1; format=flowed
>
> Dear All,
>
> I used limma with two differ…
div class="preformatted">I am analyzing 12 Agilent slides with LIMMA (ver 1.7.7, R: 1.9.1)
I load my targets file with this line...
targets<-readTargets(file="targets.txt", path = "C:/Documents and
div class="preformatted">Hi all,
I am doing some analyses of Affy arrays using limma. Following the
manual, I generated the fit2 object using the default eBayes settings,
and topTable with (almost) default
Dear all,
I?ve got the following microarray experiment design-related problem
when using Limma: In our lab we want to perform some microarray
hybridizations to identify genes whose expression is altered by a
certain...0 1
the script can be executed without error message using R (vers. 2.4.0)
and Limma (2.9.8), while the same kind of analysis in LimmaGUI
(1.10.0)
produces the…
updated 18.9 years ago • Serge Eifes
Friday, July 25, 2008 5:11 pm
Subject: Re: [BioC] Link to picture: Comparison of diff. t-statistics,
Limma and rowttests
To: Boel Brynedal <boel.brynedal at="" ki.se="">
Cc: bioconductor at stat.math.ethz.ch
>
> Dear Boel
>
>...gt; > Date: Friday, July 25, 2008 9:33 am
> > Subject: Comparison of diff. t-statistics, Limma and rowttests
>…
updated 17.4 years ago • Boel Brynedal
there,
I have an experiment that looks like factorial experiment and I want
to give
it a try to use limma for its analysis. And I have a few questions
The experimental scheme looks like this:
0: not-treated with the respective...2
replicates = 12 arrays
Here are my questions:
1. Is my experimental design suitable for limma analysis?
2. Should I combine the technical replicates before I calc…
<div class="preformatted">I am running a paired analysis with limma.
My platform is affymetrix mouse gene st.1.0 array
I have a paired group (hi, lo) with duplicates per group.
My script so far...div class="preformatted">I am running a paired analysis with limma.
My platform is affymetrix mouse gene st.1.0 array
I have a paired group (hi, lo) with duplicates per group.
My script so...Pai…
<div class="preformatted">Dear Christian,
limma 2.4.15 reads successfully all the ImaGene files which the
package authors have access to, so we can't reproduce the error...div class="preformatted">Dear Christian,
limma 2.4.15 reads successfully all the ImaGene files which the
package authors have access to, so we can't reproduce the...you
report.
I'm not ruling out a limma error, but …
<div class="preformatted">Dear Mark,
There's nothing in the limma User's Guide about continuous covariates
because they don't arise that often and because it's so easy that
there isn't...div class="preformatted">Dear Mark,
There's nothing in the limma User's Guide about continuous covariates
because they don't arise that often and because it's so easy that
there isn...s all pretty
much…
div class="preformatted">Hi Naomi,
>[BioC] | Correlation | > 1 (limma)
>Naomi Altman naomi at stat.psu.edu
>Sat Nov 12 20:54:37 CET 2005
>
>I just used intraspotCorrelation as suggested...in the online Limma
>documentation for single channel analysis.
>Over half of my estimated correlation coefficients are bigger than
updated 20.1 years ago • Gordon Smyth
behavior, piggybacking
on MArrayLM's existing behavior.
Also, is this the right place for limma questions? It doesn't have
its own mailing list yet, does it?
Thanks,
Cyrus Harmon
</div
twice: once before intervention and once
after intervention.
Which design should we use within LIMMA for assessing the effect of
the location, the effect of the intervention, and possible interaction
effect?
Thank you
<div class="preformatted">I think perhaps I was just getting confused.
The function modelMatrix() throws an error message unless the number
of
columns you want in the design matrix is one less than the number of
RNA
targets. This led me to get confused as to how you could create all
contrasts of interest if one was missing from the design matrix.
However, if we have four RNA targets (R1-…
<div class="preformatted">Hi Simon,
I understand your point, that this behaviour is inconsistent in limma.
It
is however a deliberate decision rather than a bug.
The reasoning is that a contrast is defined by c'b where c is the
contrast...div class="preformatted">Hi Simon,
I understand your point, that this behaviour is inconsistent in limma.
It
is however a deliberate decision rather…
to the proportions of up-/down-regulated genes reported in the mroast() output withinthe limma package? Documentation mentions thresholds on z. However, how could you compute the mentioned z?
 
updated 9.0 years ago • rea
Recently I have been learning limma manual, as a white letter to read the manual completely read mumbo-jumbo, there are many places do not understand, there...to see whether the chip data standardization ,then standardization using RMA methods .Finally, the limma package is used to analyze standardized data .Is my understanding correct, please?
Thanks 
Hi,
In limma's documentation, the interaction term is described as:
"The first of these questions relates to the WT.S vs WT.U comparison...Hi,
In limma's documentation, the interaction term is described as:
"The first of these questions relates to the WT.S vs WT.U comparison and the second to Mu.S vs Mu.U . The third relates to the difference of differences, i.e., (Mu.S-Mu.U)-(WT.S-WT.U) …
updated 8.7 years ago • sbcn
div class="preformatted">Hi,
I'm creating my limma design matrices by hand and am just wondering
whether the sample names in the matrix actually matter or whether they
Hi all,
I am very doubtful about the "control" method of
normalizeWithinArray function in limma package.
Suppose that I have an MAList object ma contains a two-color
array:
w = rep(1, dim(ma$M)[1])
w[ abs(ma$M) > 3] = 0
What is the difference
gt; From: Naomi Altman <naomi@stat.psu.edu>
> > Subject: [BioC] F-tests for factorial effects - limma
> > To: bioconductor@stat.math.ethz.ch
> >
> > I am analyzing a 2-factor factorial Affy experiment, with 3 d.f.
for...gt;
> > I would like to get the F-tests for the main effects and
interactions
> > using l…
updated 21.0 years ago • Ramon Diaz
steps of
reading,
normalization, filtration. Ended up on impressive heatmaps etc.
Time to move to limma, now. I've been through limma's userguide
(limma_2.18.0), chapter 7.2 (Affymetrix and other single channel
designs)
and I...was, and I am missing how to feed that info into design and contrast
matrices to operate with limma.
Is there any reading that you could recommend?
Thank you in advance.…
updated 16.6 years ago • Massimo Pinto
Hi!
This is a question regarding the limma/voom workflow for analyzing RNA-Seq dataset.
According to the workflow described in "RNA-seq analysis is easy as 1-2-3...Hi!
This is a question regarding the limma/voom workflow for analyzing RNA-Seq dataset.
According to the workflow described in "RNA-seq analysis is easy as 1-2-3 with limma, Glimma and edgeR", MDS plotting is performed on t…
Hi all,
I use limma to compare pathway score (from GSVA tool) between 3 conditions (normal control, early state, late state), I got no difference...different between normal control and late state. Would you please explain why? I thought when limma compare 3 conditions, it will pairwise compare them so if 2 conditions have different, 3 conditions also should have...I think apply limma is better…
updated 21 months ago • Chris
div class="preformatted">Dear R-Users,
I can not uderstand a result I have ( see Toptable). I used LIMMA to
find differentially expressed genes by 3 treatments, my database (
illumina files) includes (48803 probes (rows) and...after filtring tools)
k<-genefilter(detection[,81:120],ff)
# Differential expression using Limma after normalization & filtering
tools
library(lim…
updated 16.5 years ago • Mohamed Lajnef
<div class="preformatted">Hello Bioconductor Gurus,
I have the a data about gene expression from TWO COLORED Agilent
array. I
wanted to check differential expression between p3 and wild strain of
yeast.
In one array p3 is colored with Cy5 and wild is colored with Cy3 and
in the
second array the dyes are swapped. Assuming I have normalized my data
using
VSN and obtained M values for the two…
<div class="preformatted">Though I have spent many hours reading the limma user's guide, and
pored
over chapter 23 of the Gentleman, Carey et al Bioconductor book, I
have many more questions than answers regarding limma, and its use
with
our data. I come from a programming
background, with some math training (in the distant past); I am sure
many crucial statistical issues elude me. I am…
updated 19.3 years ago • Paul Shannon
<div class="preformatted">Dear List Patrons,
I am processing some microarray data obtained with Affymetrix Mouse
Gene 2.0 ST chips. Using the xps package, I have performed step-wise
RMA processing - Background correction, Quantiles Normalization, and
Median Polish summarization. The output of xps is a tab-delimited text
file with 33,960 non-log base 2 transformed expression measures, the
U…
updated 12.0 years ago • Matthew Thornton
Hey there! Hope everyone is doing well :)
I have a question regarding using LIMMA package for data that is not RNA-seq nor microarray. I have a dataset of protein/biomarker quantification(around 365...data I have can be analyzed using the same pipelines for microarrays. However, in the user guide of limma, I could not find an explanation/mention about whether limma could also be used in such set…
updated 4.8 years ago • r.i.s.alnuwaysir
Hello,
I am processing transcriptome-wide expression data using the limma pipeline. I have a two factor experiment (2 treatments crossed). My data are standardized with voom, precision weights...Hello,
I am processing transcriptome-wide expression data using the limma pipeline. I have a two factor experiment (2 treatments crossed). My data are standardized with voom, precision weights are calcu…
neeraj <kushrn at="" gmail.com="">
> To: Bioconductor at stat.math.ethz.ch
> Subject: [BioC] limma matrix design for biological replicates.
>
> hi,
>
> i am doing analysis for 10 breast cancer arrays (two color
Agilent4x44...gt; arrays) with limma,where Cy3 is normal and Cy5 is tumor.And all are
> biological replicates ,means all 10 arrays ha…
div class="preformatted">Hello all,
by using LIMMA package I'm setting the contrast matrix to discover
differentially expressed genes in a dual-color microarray experiment
updated 17.3 years ago • Erika Melissari
Hi
I'm trying to analyse some microarray data using Limma. The sample probe data is in GenomeStudio format and Limma read this nicely, but the control probes are in a table. ...When I load this into Limma I got an error:
_Error in readGenericHeader(fname, columns = expr, sep = sep) :
Specified column headings not found
updated 9.2 years ago • ctl
when I toptable the fit in limma, and set coef=1, the pvalue and padj are all 0, and coef=2 seems to be the right result, how should I understand coef=1, does it
updated 5.3 years ago • linouhao
Hi
My supervisor keeps telling me we should just use the p nominal genes from DE with limma as we don't get any FDR corrected ones. However if we do this, how do we know we are not just looking at gene expression noise
updated 9.7 years ago • chris86
<div class="preformatted">
Hi,
Chapter 7 of the limma User's Guide introduces the concept of
filtering after normalization. I'm not entirely sure how this step
should be performed...div class="preformatted">
Hi,
Chapter 7 of the limma User's Guide introduces the concept of
filtering after normalization. I'm not entirely sure how this step
should be
updated 11.9 years ago • Guest User
div class="preformatted">Hi,
I'm trying to use Limma to analyse some nimblegen methylation data on
MZ
twins (imported through Ringo).
The design is:
Two colours microarray
updated 16.8 years ago • Mario Falchi
<div class="preformatted">Hi,
Say two groups A and B. Each group has 10 individuals.
Assume that we have two variables: Y and X.
Therefore, the hierarchical linear model will like:
Yij=B0i+B1Xij+ERRORij, (i=A,B; j=1,2,...,10)
We are interested in testing the significance of B1.
Although some R packages can do this job, we are interested in
using the shrinkage property in LIMMA or other R …
3 are control), quantile normalized.
I would like to do simple differential gene expression using limma.
Is there a line or two of code that generates a simple design matrix
for
this scenario?
I usually use a design matrix created
Hi,
<span style="line-height:1.6">I have a complex design question with limma. We have 12 patients and we have several RNA seq data from each patient. PAtients have different sexes and race. From each...1\_D\_2-H) or in some cases (1\_D\_1-2\_D\_1).</span>
I am using duplicate correlation of limma/voom with blocking on patients and as for design formula I am using (~0+Labe…
nbsp; These statistics have already been computed beforehand using the limma package. "
Can someone explain me how to do that using limma ?
So I've two matrix (one containing the methylation state of each
<div class="preformatted">At 03:12 AM 6/08/2004, Richard Friedman wrote:
>Fellow Expressionists,
>
> Does Limma automatically perform a multiple
>comparison adjustment for non-orthogonal contrasts?
Yes. classifyTestsF() is a...At 03:12 AM 6/08/2004, Richard Friedman wrote:
>Fellow Expressionists,
>
> Does Limma automaticall…
updated 21.4 years ago • Gordon Smyth
Recent ...
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