a ratio)
I'm actually surprised that no "formal/mathematical" linear model is
written in the limma Users Guide... any comments?
Kind regards,
Yannick
On 2009-09-03 13:33:0, Jim Macdonald wrote:
> Hi Andre,
>
> If you want to...model selection, then limma is probably not the
tool
> for the job.
>
> Instead, what I would do would be to choose some (one, …
Order by: Relevance
Hello,
I am using limma to determine differential gene expression between healthy and KO mice. I know that there is a very strong batch effect...on this forum and on _Biostar_ that it is generally recommended to include the batch effect in the limma model instead of using for example _Combat_seq_ to adjust for the batch effect.
I wanted to make sure that limma can appropriately...effect inc…
updated 3.9 years ago • nhaus
<div class="preformatted">Dear list members,
short version of my question:
How can I determine, whether it improves the model quality of a linear
model (in limma), when I introduce additional explanatory variables?
Is
there an equivalent to feature selection (as in machine learning) for
choosing the explanatory variables?
The complete story:
We analyse a dataset of about ninety single cha…
updated 16.3 years ago • Andre J. Aberer
<div class="preformatted">Dear list,
can anybody suggest how could I insert gene names in additional to
gene
symbols on my topTable generated by limma with my differentially
expressed
genes?
cheers,
Marcos B. Pinho
Programa de Engenharia Química - PEQ
Laboratório de Engenharia...suggest how could I insert gene names in additional to
gene
symbols on my topTable generated by limma with my d…
div class="preformatted">Dear Prof Smith, dear Bioconductor's user,
I am using Limma to analyse time series microarray gene expression
data. I
have 4 time points (t1: 40 RNAs, t2:42, t3:20,t4:30). RNAs are
isolated
updated 16.6 years ago • claire pujoll
div class="preformatted">Hi,
I am using limma. Here is a error I met
SubM is a 19k by 6 matrix
> design
[1] 1 1 1 -1 -1 -1
>
PMAfit<-lmFit(subM,design,ndups=2,spacing=1,correlation
a common reference with 4 groups experimental design
by applying the same method described in the limma user's guide for
common reference 2 groups.
However, all of the reference samples were labeled with Cy5.
Therefore I multiplied
I am using limma to analyze mass spectrometry-based metabolomics data. I have a matrix of peaks (rows) by samples (columns). In this data...I am using limma to analyze mass spectrometry-based metabolomics data. I have a matrix of peaks (rows) by samples (columns). In this data, each...in this matrix might represent the ratio of 13C6-glucose to 12C-glucose across samples. Then, run limma using a s…
updated 20 months ago • c53aba27
div class="preformatted">Hi,
I have some questions about the chapter 9 in limma user's guide.
Please forgive my lack of statistical knowlege.
1. For the example in section 9.4 technical replication
updated 21.2 years ago • Ren Na
Hi,
Im currently using limma to interrogate methylation data using multiple regression models, typically in the format of methyaltion (beta) values...a benefit or difference for an OLS regression using the lmFit, eBayes and toptable functions of limma to generate results vs. using multiple testing adjusted lm function for each cg?
We've conducted both limma-based and
updated 3.7 years ago • fluentin44
Hello,
I'm working with Limma for both RNA-seq data and microarray data. I used gene read count for RNA-seq data as input for Limma. As for microarray data...to ask how can I get a matrix of log transform of RNA-seq values and microarray intensities using Limma?
I expect the result would be like a matrix with columns are the name of the sample and the rows are the genes ID/name. I know...for DE…
updated 10.1 years ago • bharata1803
gt;
>I have 2 questions:
>1. I would be really grateful to have a list of papers that cite
limma -
>does such a list exist? If so could someone send it to me.
Dear Roy,
As far as I know, there's no such list, apart from what you...cite the basic linear model paper Smyth (2004)
which explains the eBayes stuff. Many papers using limma don't give a
formal citation, unfortunate…
16:30:57 +0200
>From: "Jakob Hedegaard" <jakob.hedegaard agrsci.dk="" at="">
>Subject: [BioC] Limma - plotMA3by2 & imageplot3by2 - as -pdf?
>To: <bioconductor at="" stat.math.ethz.ch="">
>
>Hi
>
>I am very happy using the...Limma-functions
>"plotMA3by2" and "imageplot3by2" but would like
>the output as a single .pd…
Hi Guys!
I'm currently trying to perform differential gene expression analysis on Affymetrix microarray data. I'm planning on using the limma package from Bioconductor but it is not working!
I've spent the last two days trying to find a workaround for this. I've updated...differential gene expression analysis on Affymetrix microarray data. I'm planning on using the limma package from Biocondu…
updated 3.9 years ago • jaydengitt
Hey,
I have a question regarding the reproducibility of limma. I am using it for differential expression analysis for proteomics experiments. I also use the `decideTests` function...I was able to make the results reproducible by setting a seed with `set.seed`. I tried this with limma as well, but it did not resolve my issue.
Am I missing something? For example, in the `clusterProfiler::gseGO(…
updated 2.9 years ago • TSauer
Hi there,
I am trying to use limma for some rna seq data and model subjects as a random effect as I have paired samples. I have already done analysis in DESeq2...and got 400 (up and down) significant DGEs. When repeating in limma I only get 19 DGEs. I'm not sure where I am going wrong in limma - my code is below
```
counts <- DGE(counts)
condition <- factor(designTable
here means number of spots between the two duplicates)
The function duplicateCorrelation in limma can be used to estimate
correlation between within-array duplicates, the methodology is based
on the assumption that...the correlations and must take the average of the
duplicates? Are there some functions to do this in limma or other BioC
packages?
-------------------------------------------------…
div class="preformatted">Hi,
The design model is attached to this email.
I am using limma to analyze a set of microarray, but face with the
difficulty on the design matrix and contrast matrix even after reading...the
limma userguide carefully. Basically, I need to exclude the effects of
empty
plasmid transfected into the cells. Then identify
updated 17.7 years ago • Ng Stanley
Hello,
I would like to run ANOVA on my seq data using limma. I have paired samples (normal vs disease) and 3 different types of disease A,B,C.
I would like to use block=patient_block...Hello,
I would like to run ANOVA on my seq data using limma. I have paired samples (normal vs disease) and 3 different types of disease A,B,C.
I would like to use block=patient_block for paired design. Here is my…
div class="preformatted">Does anyone have the exprience to use limma for two-color array:
GoldenGate Methylation Cancer Panel I (Golden Gate Cancer Panel
Methylation Illumina)
I used it...many small
p-value the result. there are biology repeat in my data. My R code is
like this:
library(limma)
exp<-read.table("exp.txt",F)
sample_id<-read.table("sample_id",F)
row.names(exp)&…
4
Date: Thu, 25 Nov 2004 16:44:05 +0800
From: xpzhang <xpzhang@genetics.ac.cn>
Subject: [BioC] Could limma be as good as GeneSpring in nomalization?
To: bioconductor <bioconductor@stat.math.ethz.ch>
Message-ID: <20041125163802.B7A3.XPZHANG...if anyone here knows something about the software, and if this
software has more function than limma.
Thank you very much!
--
Xiaopeng ZH…
updated 21.1 years ago • Elizabeth Brooke-Powell
<div class="preformatted">Dear All:
I just started getting familiar with the use of R and different
packages to analyze liver samples. After some reading and searching I
was able to understand how to pre-process the data including
normalization with GCRMA but now I got a problem when using LIMMA and
trying to built my design.
I have 18 arrays, a group of 6 are from liver of calves that were…
div class="preformatted">
I am using limma package for identifying differential expression of
affymetrix .CEL file. I used quantile normalization method and...saved
the normalized data in .txt file. However, i am not able to import the
.txt file into limma for differential expression.
Kindly tell me the sequential procedure for identifying the
differential expression
updated 12.3 years ago • Guest User
div class="preformatted">Dear Sir/Madam,
I meet some problems when I use the limma package to analysis the
Agilent
single channel microarray. I got 8 samples (with 8*60K array) results
as
following:
Samples...2
4
6
6
2
2.5
6
6
DOWN
0.01
2
DOWN
0.02
1
DOWN
0.2
My R script as follow:
library(limma)
targets <- readTargets("targets.txt")
x <- read.maimages(target…
updated 12.8 years ago • yong li
Dear members,
I encounter two problems when analysing the microarray data employing
the
package limma. I am using R ver.2.4.1 and limma ver.2.9.13.
-------Question 1-------------
After the backgroundCorrect step, the software gives a series
updated 18.8 years ago • De-Jian ZHAO
Hi,
I'm going to use limma squeeVar function to estimate protein variance, for the input sample variances and degrees of freedom for the sample
updated 7 months ago • Mengchun
DAY 30 (REPLICATES)
SAMPLE 18 MEDIA D (DAY 90 (REPLICATES
I am new to R and would like to use limma for identifying
differentially expressed genes. I have read the limma users guide
(Gordon Smyth), LAB4 limma 2005, James...BioC 2009.
(I am afraid my linear algebra is not good.)
I tried the lumi script for a modified limma (PanDu et al 2009)
but met no success as I do not kn…
example, I have a data table with n rows (peptides) and m columns (replicates). I would like to use limma to do a differential expression of each peptide versus a constant of one. This should be a generalisation of a one-sample...of ones to my data and marked it as a separate condition, as in this generated example.
library(limma)
set.seed(1)
ndat <- 10
nrep &…
class="preformatted">How would I import a tab delimited file containing geneids and
logratios
into limma for analysis without going through the low-level reading,
normalizing of the cel, gpr, etc. files? Thank you.
Karen Vranizan
Dear R users,
I have a project that needs to use linear model of limma to do the contrast analysis, but the difficult is to use numeric variable in the contrast. We would like to use Batch as...represent the post-infection) to 0 (pre-infection), I don't know if there is a way to solve this in limma or other package.
Thanks a lot and appreciate it for any input.
Best,
Li
 
updated 11.2 years ago • jial2
<div class="preformatted">Hi, Naomi:
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 first part of my experiment consists of a loop design to compare
the gene expressi…
sense are related and form a block. There are no technical
replicates within each block.
I am using limma. In the model I calculate separate coefficients for
each of the 16 conditions. I then use contrasts matrices to evaluate
got error messages whenever I try. Any help
will be greatly appreciated!
In R help for package limma, it said
MA.RG converts an unlogged RGList object into an MAList object.
MA.RG(object) is equivalent to
normalizeWithinArrays
Hi,
I need some help with the interpretation of B statistics generated by
eBayes in the limma package.
I want to compare gene expression in three groups of Affy samples. The
probe level data was generated from .cel
div class="preformatted">Hi,
In limma, what is the best way to automatically generate a contrast
matrix
with all possible pairs? For example, if I have 4 groups
class="preformatted">Hi I just wanted some advice on analyzing single channel data from
Genepix in Limma.
There are a number of slides that have bad cy5 signals and other chips
where on cy3 was used, so I wanted to be able to just...says use this:
y2 <- normalizeBetweenArrays(RG$G, method="quantile")
(or use vsn)
and then run Limma normally.
I was wondering if this is still the prefe…
updated 18.7 years ago • Lance Palmer
Dear all,
thanks a lot for supporting such nice packages. I would like to know if limma fit function could be used with smaller set of genes or other metabolites quantified by liquid chromatography. I use...limma in genes lists with thousand of genes, and never used with smaller features. I wonder if the moderated t-test could be used...Can we use empirical Bayes moderation in this situation? If…
updated 8.5 years ago • iglezer
if I normalize to the "real" \# of reads I can overcome this problem, but I would have to feed into limma-voom pipeline (below).
__Q1:__ where in the limma-voom pipeline (below) should I modify to prevent it from trying...to normalize?
__Q2:__ if there are an unequal \# of reads that limma "sees", or if I remove "voom" when it tries to do the model, does t…
updated 9.2 years ago • tealfurn
Hello,
My name is Mahes Muniandy and I am a doctoral student working on twin data. I have used limma previously for gene expression as well as methylation data and would now like to use it on my metabolomics data - to detect...is or should I reduce the data to PCAs and then use the PCA values to represent my metabolites in my limma model?
Here is my design matrix:
<code>design …
updated 8.7 years ago • mahes.muniandy
<div class="preformatted">> Date: Sun, 7 Aug 2005 20:37:22 -0700
> From: davidl at unr.nevada.edu
> Subject: [BioC] Limma using all probes on Affy chip
> To: bioconductor at stat.math.ethz.ch
>
> Hello,
>
> I'm sorry if this question went to the wrong place, but I would
be ecstatic
> if someone had the answer to it. I've …
updated 20.4 years ago • Gordon Smyth
However, after reading in the gpr files via the following,
carrying out analysis as described in the limma guide, and generating
a
list of the top 100 DE genes via Bayes, I am still getting flagged
genes in the final output.
Shouldnt
div class="preformatted">Hi all,
I'd like to use limma to identify a possible interaction between two
drugs
(called "x" and "y") which would be reflected in gene expression.
That
div class="preformatted">Hi,
I am having problems fitting the following model into limma, I have
tried many different ways of specifying the design and contrast matrix
but they all seem nonsense so I won t post
<div class="preformatted">Hi,
I too would find it useful to have the CI reported.
Thanks,
Corrinne
-----Original Message-----
From: bioconductor-bounces@stat.math.ethz.ch [mailto:bioconductor-
bounces@stat.math.ethz.ch] On Behalf Of Gordon K Smyth
Sent: 30 October 2010 00:13
To: Timothy Wu
Cc: Bioconductor mailing list
Subject: [BioC] limma report logFC confidence interval?
Sunny's CI …
updated 14.9 years ago • Segal, Corrinne
can not
do those. Also, GCOS can only compare two chips at a time. Here is
what I
know:
The Limma package needs the data to be in an object of the class
"exprset"
with the samples as columns and the genes as rows. If I use...for
all the
arrays with the probe sets (instead of expression values) as rows that
I could
plug into limma. I'm aware that some probe sets have more probes than
oth…
updated 20.4 years ago • davidl@unr.nevada.edu
div class="preformatted">Hello,
I want to analyze a recent Affymetrix Exon array dataset with the
limma
package; I imported values from APT and created and ExpressionSet with
it, but the experiment's design is not the simplest...the same blood donor, so i'd like to capture this effect in
the data to improve p-values. I did a limma analysis using
onechannelGUI
(with great results) but it doesn…
all
I have a problem about understanding procedure of quantile and scale
normalization techniques in limma package
How can i observe steps of them in software? Is there any command?
Thanks in advance
--
*S. Fazeli
MSc Student of Chem
to use the median signal measurements and the
column definition in the read.maimages function in limma (I'm using
v2.16.4) source="agilent" is G = "gMeanSignal",Gb = "gBGMedianSignal",
R
= "rMeanSignal", Rb = "rBGMedianSignal".
Thanks for...February 04, 2009 4:10 PM
To: Coleman, Ilsa
Cc: Sean Davis
Subject: Re: [BioC] read.maimages(limma) source="agilent" updated for
20-bitscanner?
In my experie…
Hi all
- I use limma to do the differential expression analysis, I want to do the volcano plot, x-axis is logFC and y-axis is `-1*log10(adjust p...Hi all
- I use limma to do the differential expression analysis, I want to do the volcano plot, x-axis is logFC and y-axis is `-1*log10(adjust p)`. But I found the the adjust p output by limma is so small and after -log10 transfor is up t…
updated 6.8 years ago • xingxd16
expression analyses for multiple but similar studies. Is there a way to perform a meta analysis with Limma results?
Thank you so much
updated 9.0 years ago • Annie Li
Richard Friedman <friedman at="" cancercenter.columbia.edu="">
>Subject: [BioC] B value cutoff in LIMMA
>To: "bioconductor at stat.math.ethz.ch List'"
> <bioconductor at="" stat.math.ethz.ch="">
>
>Dear Bioconductor List...gt; In an earlier posting, Gordon Smyth recommended
>a tentative cutoff of B>=0 for Limma output.
&…
div class="preformatted">Can I suggest that limma package returns the posterior probabilities
along with the log odds ratio, B ?
I am currently using the following codes
a common reference with 4 groups experimental design
by applying the same method described in the limma user's guide for
common reference 2 groups. However, all of the reference samples were
labeled with Cy5. Therefore I multiplied
div class="preformatted">Dear limma experts,
I have direct experiments with two biological replicates and two
technical replicates. In each array sots
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
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
Recent ...
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