But in fact,
they can be estimated just using data from other 9 patients.? Is there
a way to tell limma to do that?
Thanks!
Tao
library(limma)
dat <- matrix(rnorm(400), ncol=40)
ptID <- factor(rep(1:10, each=4))
day <- factor(rep(1:4,10))
dat
Order by: Relevance
div class="preformatted">Hi,
I have been analyse a time course experiment with limma and I get the
end of section 16 in userguide very well.
But, I don't know how do I do to get the names of genes differentially
I have been analysing protein array data with hundreds and thousands of proteins using Limma in R.
For normalisation I have been using the following:
y <- normalizeBetweenArrays(log2(exprs), method="quantile")
followed...plots and density plots for QC. Followed by model fitting for differential expression analysis in Limma.
However we then chose the most promising 35 prote…
updated 7.0 years ago • reubenmcgregor88
Hello,
I am using limma to determine differential gene expression between healthy and KO mice.
In my design matrix, I am including several...Hello,
I am using limma to determine differential gene expression between healthy and KO mice.
In my design matrix, I am including several covariates that I know influence gene expression, but that I am not interested in.
Specifically, it looks s…
updated 3.9 years ago • nhaus
Hi all,
I'm using voom and limma to analyse RNAseq data. I'm comparing the percentage distribution of reads among different categories of transcripts...little difference? I'm unsure if the normalised counts can be used for purposes other than in the limma pipeline or if they should be multiplied by the normalisation factors first?
Any advice/experience much appreciated
updated 11.2 years ago • Peter Crisp
br/>
Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1</code>
With limma, I am fitting :
`` fit <- limma::lmFit(grp2$getNormalized()$data, ``model.matrix(~ Condition + BioReplicate, grp2$annotation\_)`` ) ``
<code...fit.eb <- limma::eBayes(fit)<br/>
limma::topTable(fit.eb)</code>
But topTable produces an output sim…
plotMDS(), and the data are
nicely intermixed as one would hope. Now I need to do DE
analysis with Limma. Hsu (the first 26 samples) are experimental
and Kai (the last 10 samples) are control. So I create a design
matrix like this
updated 12.6 years ago • Ed Siefker
lm(y ~ d + X) ## C. using covariates
```
I am now aiming at applying this to mRNA analysis using a `limma/voom` approach. I was suggested to multiply `voom` weights with the IPW weights `w` which seems reasonable and is basically...count[keep,,drop=FALSE], design, weights=w)
fit <- lmFit(v, design, weights = v$weights*w) |> limma::eBayes(robust=TRUE)
```
This seems to work well. …
updated 2.9 years ago • jay
Hi,
I am using Limma to analyze my data, which is a simple two-group comparison (treated vs. control). The analysis is very straigtforward, but
updated 8.5 years ago • Wu, Xiwei
What is the recommended way of calculating a standardized effect size for each gene in limma, preferably based on the fit object returned by `` lmFit ``? Possibly, would that be something like
<pre>
f$coefficients / f$stdev.unscaled
updated 4.8 years ago • January Weiner
all,
please would you advise : could the normalization methods (TMM, etc) that are implemented in limma or edgeR (or DESeq2, or in other packages) be used for the normalization of 5C interaction data ? thanks,
-- bogdan
 
08 +0100
> From: Georg Otto <georg.otto at="" tuebingen.mpg.de="">
> Subject: [BioC] Question: limma decideTests nestedF p-values
> To: bioconductor at stat.math.ethz.ch
>
> Hi!
>
> I am using decideTests with the
<div class="preformatted">Hi,
I tried to use imageplot to see my normalized data in limma package, I
tried
both command as following,
> imageplot(log2(RB$Rb[,1]),RB$printer,low="white",high="red")
and
> imageplot(MA$M...div class="preformatted">Hi,
I tried to use imageplot to see my normalized data in limma package, I
tried
both command as following,
> imageplot(log2…
on my covariates of interest in my samples (a human longitudinal study) on which I am going to run limma.
Multiple imputations in R give multiple datasets. Is it advisable to run limma using each of these imputed datasets...and then average the estimates somehow that I get from limma or is there a better way of doing this that I am missing out on?
The missingness is between 10 to 13% in these c…
updated 2.8 years ago • S
Hi @gordonsmyth,
I am using limma to perform standard analysis on an RNA-seq dataset. I colleague asked if I could do a test of differential variance between...than for another subset. I could use `var.test()` built into R, but I figured that I could use limma to account for covariates and do the test on residual variance. Moreover, I'm thinking I can take advantage of the empirical
updated 3.1 years ago • gabriel.hoffman
div class="preformatted">Dear All,
I have analyzed a dataset for differential gene expression using
LIMMA. The requirement was to select probesets with highest value of
expression. I notice that there is a change in results...for when i
filter for probesets before and after performing LIMMA. The logFC and
gene list remains the same, only change is in the p-value and B Value,
again this is pos…
way to judge this, look
at the component fit$df.prior after you use the eBayes() function in
limma. The better you stabilise the variances, the larger will be
df.prior and the greater will be the power to detect DE genes...2006 16:46:15 +0100
>From: Pie Muller <pie.muller at="" liverpool.ac.uk="">
>Subject: [BioC] LIMMA: choice of offset value for background
> c…
<div class="preformatted">Hi Johannes,
I would like to explain my data in detail for your deep understanding.
There are three replicate data from two-channel microarray
Two of them were scanned by genepix scanner and the other was scanned
by
agilent scanner.
All of them are originated from same microarray platform( agilent chip
). Just different scanner makes them provide different outpu…
updated 14.2 years ago • 이선재
gt; Natalie
>
>
> BTW: I also have 4 practicals that I use to teach the fundamentals
of
> limma (they include RBasics, LimmaBasics, LimmaPreprocessing,
> LimmaDiffExpression). These have a lot more detail for real...beginners
> to R who are trying to use Limma. The examples are complementary to
> the LimmaUsers guide, but they include more detail…
div class="preformatted">Hello Everyone,
I am having problems using limma to analyse my data. It seems that
when executing the function read.maimages() over the data it gets read
wrongly - the values
at="" biologie.uni-freiburg.de="">
> To: bioconductor at stat.math.ethz.ch
> Subject: [BioC] Limma: How to analyze 1- and 2- colour Agilent
>
> Hello all,
> I have a special Agilent 4x44 K microarray analysis problem.
>...if necessary. Finally, model and extract
> contrasts.
>
> The alternative was to fool Limma into reading red and…
updated 15.1 years ago • Gordon Smyth
<div class="preformatted">Actually on thinking about it a little onger, I can't see any reason
why the fixed effect approach
for Patient is not also correct here, if correctly implemented. The
random effects (blocking)
approach is theoretically more powerful, but makes more assumptions.
Gordon
>>Date: Sun, 17 Jul 2005 12:05:41 +0200
>>From: "Johan Lindberg" &l…
I am using Limma for downstream analysis of mass spectrometry proteomic data.
I am comparing differential protein expression between...subtype, batch, age & sex. I wish to adjust for batch (A-E), as well as sex and age.
I read the Limma user guide and searched the Bioconductor support pages- both of which I found very helpful.
From my understanding, it...below.
My question: Is it po…
updated 2.6 years ago • sarah.kelliher
<span style="line-height:1.6">I'm currently using the excellent camera/roast/romer functions from limma for analysing groups of genes in count data.</span>
Currently there are (to my knowledge) two different ways of calling the...span style="line-height:1.6">I'm currently using the excellent camera/roast/romer functions from limma for analysing groups of genes in count data.</s…
div class="preformatted">HELLO!!
I would need some help about R/Limma, if possible. Does anyone have a
code
example for 2x3 factorial design to show me? I have some trouble in
writing
it. I hope
updated 18.5 years ago • Alessandro Fazio
preformatted">
Hi everyone,
I'm working on an analysis of illumina microarrays and am using the
limma package. But looking at the code provided with the vignette
there doesn't seem to be a summarization step (where multiple
<div class="preformatted">
Begin forwarded message:
> From: Sean Davis <sdavis2@mail.nih.gov>
> Date: October 1, 2004 1:29:57 PM EDT
> To: "Matthew Hannah" <hannah@mpimp-golm.mpg.de>
> Subject: Re: [BioC] ULYSIS Alexa Fluor labelling kit / dye bias /
limma
>
> Matt,
>
> Ah, I see what you are saying. Yes, limma can (and…
updated 21.3 years ago • Sean Davis
support.bioconductor.org/p/107787/) but I wanted to check this information was up to date and that limma/voom is the best option for this.
2. **Is there a method that will allow me to use more complex random effect specifications...I understand that limma-voom's `duplicateCorrelation` and the dream functions from `variancePartition` will only allow for random intercepts
updated 4.5 years ago • jackgisby
<div class="preformatted">Hi,
I'm using Limma to find differentially expressed genes in a set of 2
replicate two-colour arrays, and I would like to know precisely how...div class="preformatted">Hi,
I'm using Limma to find differentially expressed genes in a set of 2
replicate two-colour arrays, and I would like to know precisely
normalized in the nSolver Data Analysis software. I have the normalized data, and would like to use `limma` for further analysis like filtering and statistical modelling. I would like to perform filter by expression on the...normalized data matrix, it seems like in `limma` this type of filtering could be performed only on the raw data (counts). Is there a functionality that I can use this normali…
updated 3.3 years ago • mohammedtoufiq91
<div class="preformatted">Dear Ross,
Short answer:
The vst transformation is asymptotically equivalent to the log2, and
2^logFC is the correct transformation.
Longer answer:
See
http://www.ncbi.nlm.nih.gov/pubmed/20929874
for why vst gives small fold changes, and what you should do about it.
BTW, there is nothing "linear" about raw scale intensities for
fold-changes. The logFC ar…
updated 13.9 years ago • Gordon Smyth
div class="preformatted">Dear limma experts
During creating the pipe-line for dissecting differential gene
expression
in frame of limma,
several questions
updated 13.9 years ago • Vladimir Krasikov
div class="preformatted">
Hi, List:
I have a question regarding paired samples test in limma package.
Here is what I got
####W and B are race
####T and N are tumor and normal(paired by same Samples), respectively
####Samples are...individual patients: tar$AccNum########
####
> library(limma);
> tar<-readTargets("Test_Desc.txt");
> mydata<-read.delim("Test…
vs sensitive to drug X, control vs insensitive to drug X, and sensitive vs insensitive. I used limma to find related DEGs, here is my codes
fit <- lmFit(data, design)
keep <- fit$Amean > median(fit$Amean)
ebayes <- eBayes...factor(sensitivity$chemosensitivity)Rx Sensitive"
Now from limma output, I found genes with negative log fold cha…
<div class="preformatted">Hello to everyone!!
I've been using RMA to normalize my data and LIMMA to obtain a list of
significant genes. My design was a 2x2 factorial design with 4 groups:
Diabetic treated, diabetic untreated...div class="preformatted">Hello to everyone!!
I've been using RMA to normalize my data and LIMMA to obtain a list of
significant genes. My design was a 2x2 factoria…
updated 21.8 years ago • Jordi Altirriba Gutiérrez
of disease in diet)
> Diet.disease vs. nodiet.nodisease
> I used makecontrasts function in limma in R.
> Contrast.matrix=makecontrasts(
> Diet.nodisease vs.
nodiet.nodisease= Diet.nodisease - nodiet.nodisease
that an answer was given:
Should Illumina methylation beta data be transforrmed before input
into Limma.
Beta values are between 0 and 1.
In ordinary frequentist statistics variables which range between 0 and
1 are subject...model).
Should
A. A logistic transformation be applied before inputing methylation
beta data into Limma.
or
B. Should a log transformation be applied.
or
C. Should some othe…
Testing for logFC significantly larger than threshold; or: calculating confidence intervals in limma
between the experimental
conditions (expressed as logFC) is significantly different from 0.
Thus, limma provides a p-value (or adjusted p-value) for the test
where the H_0 is that logFC == 0, and H_alt is that logFC =/= 0.
I would like, however...the
regular t-statistic, but I would like to take advantage of the
moderated t-statistic present in limma as well as all the facilities
for creating co…
hello everyone
Am trying to do DEG analysis in limma. Since am new to this i want to know how to normalize the data(GEO GSE matrix file). My data contains different time course...time point within the data.Can anyone suggest me codes to run GEO matrix file in Rstudio using limma.
Thank u
updated 7.5 years ago • devarajsaranya
<div class="preformatted">I am a bit late on this discussion, but here is my input:
We are using EST arrays, which have similar problems. We use a few
spike-ins (3-10), spotted many times each. (We are using 50
spots/spike-in, but I think 25 would be sufficient.) We spike them in
a
titration series, which helps us determine how well the loess works
(versus
"A"). Having many replicates …
updated 20.5 years ago • Naomi Altman
if necessary. Finally, model and extract
contrasts.
The alternative was to fool Limma into reading red and green channels
of the 2-colour data into an EListRaw, combining with the 1-colour
data, and normalizeBetweenArrays
updated 15.2 years ago • Edwin Groot
Hello,
I think the limma guide is pretty good... however, I don't really understand from it how to get very rough data into shape (and what shape is...Hello,
I think the limma guide is pretty good... however, I don't really understand from it how to get very rough data into shape (and what shape is needed...array is which sample, and which row came from where. What I do not know is how to read …
updated 9.4 years ago • sumneuron
Hello,
I have a question regarding the vennDiagram function in the limma package.
I'm trying to make a Venn Diagram comparing 3 groups relative to a control (4th group). I.e. group 1 vs group 4, group
updated 6.9 years ago • MicheK
\*Question posted as new question thread as requested by [Aaron Lun](https://support.bioconductor.org/u/6732/)\*
Dear limma team,
First of all, I want to thank you for this wonderful package. This said, I need to ask you a question on the subject mentioned in this post, Standard error calculation from my___ fit ___object using the command in the post:
<pre>
>std.error = …
updated 9.5 years ago • José Luis Lavín
Dear all,
Using the limma package I compared the mRNA expression profiles between small groups (N=5) of isogenic mice (balb/c) for different conditions...questions:</span>
<span style="background-color:rgb(249, 249, 249)">1) Do I need to adapt sepcific limma functions to take this study design into account? </span>
<span style="background-color:rgb(249, 249, 249)"…
I'm sure this is an easy question, but I'm fairly new to using limma and R and I'd appreciate any help or guidance. I've run a paired limma analysis trying to look at differentially expressed
I installed limma and then when using duplicateCorrelation() I get an error which includes:
_Error in duplicateCorrelation ..._
_ statmod
updated 9.6 years ago • nathan
and the other is tumor tissue of the
same
subject.
I am following the code as mentioned in the Limma User guide,p.40,8.3
Paired Samples)
Code:
>source("http://bioconductor.org/biocLite.R")
>biocLite("limma")
>library(limma
Dear List,
Is voom by group available in limma?
When I type the command it does not seem to be there.
```> library(limma)
> voomByGroup
Error: object 'voomByGroup' not found
<div class="preformatted">
Hello,
I am trying to use Limma for background subtraction and then marray
for normalization. I am confused about why normalization is
introducing NA values.
This happens regardless of which background subtraction and
normalization methods I use - even edwards, which does not produce ANY
negative fluorescence values after background subtraction. The only
way to …
updated 12.7 years ago • Guest User
to go through your code in detail.
I agree that you have a split plot design. My understanding of limma
is that it handles 1 random effect. In the split plot design you
describe, you should test disease status against subject...you are a very active member of the Biocond mailinglist,
>especially for questions on the use of limma for any kind of
>experimental designs.
>I ap…
Hi,
I have an experiment where I have treated a cell line with two drugs A and B, their combination AB, as well as control C. So I have 4 treatments but also 3 time point time=3,9 and 24 hours. At each condition and time point i.e. A\_3 I have 3 treatments. My goal is a dynamic analysis as such at each time point (3,9,24) and treatment (A,B,AB) I want to find DE genes wrt to control C at that ti…
chips. I wanted to find which genes are differentially
expressed when exposed to ethanol. Using the limma using guide I have
got
this code so far
====================================================
files <- c("E2h_1.CEL", "E2h_2.CEL", "E2h_3.CEL",
"E2h_4.CEL","W05h_1.CEL", "W0h_1.CEL", "W2h_1.CEL
<div class="preformatted">hi,
i am doing analysis for 10 breast cancer arrays (two color Agilent4x44
arrays) with limma,where Cy3 is normal and Cy5 is tumor.And all are
biological replicates ,means all 10 arrays have been prepared from 10...hi,
i am doing analysis for 10 breast cancer arrays (two color Agilent4x44
arrays) with limma,where Cy3 is normal and Cy5 is tumor.And all are
biologi…
<div class="preformatted">Hi Gordon,
I've been out for a while and finally read your detailed reply.
Thanks so much - it really helps clarify things for me!!
Cheers,
Jenny
At 05:55 PM 11/27/2008, Gordon K Smyth wrote:
>Hi Jenny,
>
>Should blocks be fixed (in the design matrix) or treated as random
>(hence enter the covariance matrix as correlations)? This que…
![enter image description here][1]
Hello everyone,
I'm trying to analyse microarray data from Affymetrix. I am analysing a study in GEO database with a number:GSE49893. Unfortunately I have stumbled upon a problem. When using a 'alias2SymbolUsingNCBI' function the output is showing that GeneID, Symbol and type_of_gene is 'NA'. When I checked the eset data by going into featureDATA and then …
updated 3.6 years ago • Prometheus405
<div class="preformatted">Hi Qin,
On Thu, May 13, 2010 at 11:38 AM, qin kuang <kuang_qin at="" hotmail.com="">
wrote:
> Thanks Steve.
>
> Actually I have done this family by family. I also tried method like
GEE to
> take familial relationship by averaging technical replicates. At
this point,
> looks the methods like LIMMA/GEE can not? two-level/type…
Dear Al,
No research papers (to my knowledge) have been written yet on multiple
testing for the hierarchical linear model, so I can't refer you to any
literature.
Use "separate" if you want to get the same results as topTable(). The
great advantage of this method is that you'll get the equivalent
results
regardless of which set of contrasts you test together. This is fine
for
each contrast bu…
<div class="preformatted">Hello,
I found that the question was already answered, but the solution
proposed did not work for me.
Could you please help to resolve an issue with limma I faced. Please
see the attachment. I have a set of arrays for 4 groups of patients
(Atype) taken at two time points (Visit). Every...but the solution
proposed did not work for me.
Could you please help to res…
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