class="preformatted">Hi,
Maybe a naive question, but is it possible to do a 'one sample t-test'
in limma while including a covariate in the model? If so, how?
I have an experiment in which 32 volunteers were profiled on array
Order by: Relevance
<div class="preformatted">Dear limma users,
I am trying to analyze a 2x2 factorial experiment with Agilent two-
color
arrays (with direct design). I noticed (from...div class="preformatted">Dear limma users,
I am trying to analyze a 2x2 factorial experiment with Agilent two-
color
arrays (with direct design). I noticed
height:1.6">I'm trying to analyze 8x 60 k Agilent data using the latest version of Bioconductor and Limma in Rstudio (MacOSX, Yosemite). I read in the microarray data using the following commands:</span>
targets<-readTargets...One month ago, I ran exactly the same commands/script but with an older version of Bioconductor/Limma and BOTH RED and GREEN channels were plotted back the…
updated 10.8 years ago • wd
Dear ALL,
i would like to use the function treat implemented in limma, in order to test simultaneously the test significance of my microarray linear model fit and my design. Because i have
updated 10.8 years ago • svlachavas
treated I see a lot of differences, so is correct to
> apply a 2 x 2 factorial design?
> Is LIMMA the correct tool to answer my questions? If it is the
correct
> tool, how can I do a factorial design matrix (if to do a factorial...CC: bioconductor@stat.math.ethz.ch
>> Subject: Re: [BioC] Multifactorial analysis with RMA and LIMMA of
>> Affymetrix m…
updated 21.4 years ago • Peter Lee
List,
I have a question regarding what weighting function to use when
analyzing Agilent data with limma. My question is whether or not it
makes sense to down-weight the control probes?
I have defined a weighting function:
wtfun.Agilent
updated 14.0 years ago • Daniel Aaen Hansen
lt;- model.matrix(~ 0 + f)
design
colnames(design) <-c("Healthy","unaffected")
design
library(limma)
fit <- lmFit(eset, design)
library(hgu133plus2.db)
fit$genes$Symbol <- getSYMBOL(fit$genes$ID,"hgu133plus2.db")
contrast.matrix
updated 11.1 years ago • Roopa Subbaiaih
genes analysis. From the results I see a general difference in logFC values for genes from limma-voom, edgeR and DESeq2. Although some people saw difference in logFC between edgeR and EDSeq2 and got good answers (see...p/75330/)), in my case edgeR and DESeq2 get very simmilar results but quite different from limma-voom.
I found that (not sure, i saw it somewhere)
limma's logFC =mean(l…
div class="preformatted">I am analyzing in limma a two-color array experiment where I am
compare 4 conditions: Wild-type (WT) versus Knock-out (KO) x Normal
(NORM) versus Stress
255))
It works better from normalized data set, but, I would like to run it
on
eBayes object from limma. Is it possible? I would like to see my all
data, because I have a lot off methabolics pathway and we is very
curious to see
if you
could
share your experiences on ways to 'filter' data using spot quality
weights for use in limma, specifically whether it is smart to filter
on
intensity of the respective channels in relation (or not) to the
respective
using the median of all samples).
we can see in the geo website, it has geo2r script, all used limma, no matter what happened, just sometimes use log2 when found too huge values, so is it suiatble for limma to do so,
especially
updated 5.3 years ago • linouhao
regarding the analysis of my microarray data. I am pretty new to gene expression analysis, and `limma` seems to be a very powerful package, but I am still a bit overwhelmed by it because it offers so many different functions...So far, I have been inspired by chapter 17.4 (Time course effects of corn oil on rat thymus) of the [`limma` Handbook][1]. Here, however, the data are not normalized to a c…
updated 3.2 years ago • Sam
by Imagene image
analysis. I have a trouble in loading the data to do normalization
using limma.
> library(limma)
> targets<-readTargets("targets.txt")
> targets
SlideNumber FileNameCy3 FileNameCy5
1 12 MB72
div class="preformatted">Hi all
I am trying to utilise Limma to analyses data from a two colour
environmental microarray in an experiment that is investigating
microbial function...targets2$channel.col)`
[1] "contr.treatment"
> # next do intraspot correlation ...
> library(limma)
> corfit<-intraspotCorrelation(MA,design.sc)
Loading required package: statmod
Warnin…
updated 5.1 years ago • Ross Chapman
All,
I am relatively new to R and bioconductor. I would like to know if
there is a way to alter LIMMA defualt options such that the package
instead of averaging signal intensities of probesets selects the
probesets
div class="preformatted">Hi list,
In the limma userguide it says at the end of section "8.1.2 Dye Swaps"
(page 34): "The fold changes and significant tests in this list are...graphics" "grDevices" "utils" "datasets"
"methods"
[7] "base"
other attached packages:
limma
"2.9.17"
Am I doing something wrong?
Thanks for any help,
Karsten
</div
updated 18.7 years ago • karsten_hokamp@sfu.ca
<div class="preformatted">Dear Sarah,
Just put Pairs in the design matrix, for example
model.matrix(~Groups+Pairs)
and use duplicateCorrelation() for the biolreps.
Best wishes
Gordon
> Date: Tue, 1 Oct 2013 17:55:34 +0200
> From: Sarah Bonnin <sarah.bonnin at="" crg.eu="">
> To: "bioconductor at r-project.org" <bioconductor at="" r-project.org="">
&a…
<div class="preformatted">Dear Charlotte,
Paired samples are normally handled as described in Section 8.3
"Paired Samples" of the limma User's Guide. There shouldn't be any
conflict between this and your technical replicates.
Best wishes
Gordon
>Date: Wed...Charlotte,
Paired samples are normally handled as described in Section 8.3
"Paired Samples" of the limma User's Guide. There…
interested in. I am
guessing that you have Affymetrix microarray data. There is an
example in
the LIMMA User's Guide (in the development version, not the BioC 1.2
release) in the section on Affymetrix data which fits your data
updated 22.3 years ago • Gordon Smyth
Dear all,
I am having some conceptual issues with the contrasts generated by limma. From my understanding, contrasts acts as an method for defining comparisons between groups. For example, we have expression...interesting
To this end, I thought of generating contrasts using the makeContrasts() function in limma. However, I thought that defining contrasts was conceptually the same as extracting …
updated 10.2 years ago • Andy91
<div class="preformatted">
Dear Paul,
> Date: Thu, 5 Jun 2008 13:42:40 +0100
> From: "Paul Geeleher" <paulgeeleher at="" gmail.com="">
> Subject: [BioC] Do my Limma results look "normal"?
> To: Bioconductor <bioconductor at="" stat.math.ethz.ch="">
>
> Hi,
>
> This is the first time I've ever...42:40 +0100
> From: "…
updated 17.6 years ago • Gordon Smyth
there is probably a good reason for it, may I know why that is, and whether this makes sense with limma?
[1]: https://bioconductor.org/packages/release/workflows/vignettes/RNAseq123/inst/doc/designmatrices.html#cyclical
updated 3.1 years ago • ATpoint
Hello all,
I was using limma for assessing the deferentially expressed genes in my microarray experiment. However, during the analysis process
updated 9.5 years ago • venu
Hi everyone,
I have some doubts about the removeBatchEffect function from the Limma package.
I am working on association of expression data (RNAseq) with a continuous phenotype variation (instead of a...Hi everyone,
I have some doubts about the removeBatchEffect function from the Limma package.
I am working on association of expression data (RNAseq) with a continuous phenotype v…
updated 7.2 years ago • dressa_ol
div class="preformatted">
Hi,
I don't known the argument in makeContrast function of limma
package.
Says:
contrast <- makeContrasts("X - Y", levels=design)
I known that X can be Treatment and Y the Control, but what is
updated 14.3 years ago • Paz Tapia Ramirez
character
settings either in the GPR file or in your version of R. This is an R
issue rather than a limma issue.
Best wishes
Gordon
> Date: Thu, 17 Dec 2009 12:13:56 +0100
> From: Chris Fenton <chrisf at="" fagmed.uit.no="">
> Subject...BioC] LIMMA problems with gpr file (ATF indentifier ?)
> To: bioconductor at stat.math.ethz.ch
> Message-ID: <1…
div class="preformatted">
Dear all,
I am analyzing data from 44k agilent microarrays in limma. I
have
several issues where I'd like to hear some opinions from others.
First, I have put the weights of the controlspots
a replicated time course experiment with three time points. This is dealt with in detail in the limma User's Guide in Section 9.6.1 "Replicate time points". You should be able to apply the advice in that...nbsp;section to your data without any problems.
The limma User's Guide tells you that spline curves are only for time course experiments …
updated 11.1 years ago • Gordon Smyth
div class="preformatted">Dear Bioconductor users.
I am using gcrma and limma on a dataset of 3 conditions with 2
replicates
each.
1. First I normalized 2 conditons together (4 arrays) and got 312
probesets...with B>0
using limma comparisons. I used no filtering.
2. Then I normalized all 3 conditions together (6 arrays) and
compared the
same 2 conditions
argument uncompelling.
A search of the archive produced several discussions of missing values
in limma. The main argument I see is Gordon Smyth's (Date:
2008-03-08)
"The ideal solution is not to introduce missing values into your
div class="preformatted">I am trying to use limma for the analysis of 2DGE proteomic data and
am
having great difficulty constructing the design and contrast matrices
I have a few queries regarding Agilent data processing by Limma package.
1) I tried to test the use-case describe in Limma package vignette " Time Course E ects of Corn Oil on Rat Thymus with
I look for a significant difference in slopes or how do I best model this? (should be possile in limma or would I need some kind of mixed-effects model using lme4 etc. ?)
How would I build the formula for the model in limma and
updated 8.1 years ago • biominer
1
```
I want to compare within the genotype as well as time-course. I've been following the Limma section 9.6.1 (Time course with replicates) and my strategy looks like:
```
> colnames(design)
[1] "Tam.0d" "Tam.1d" "Tam.3d" "Tam.5d
updated 6.6 years ago • ivan.vechetti
div class="preformatted">Hi BioC,
I have basic question regarding How Limma contrast
statistics work when I have situation like below:(I am
using Affymetrix CEL files, with 4 diff. groups)
> design
p-value adjustment for multiple testing across
contrasts.
Let's say we have three groups, as in the Limma user guide, section
8.6,
and this contrasts are closely related one another, so we want to
apply
method="global" to decideTests
Hello,
I have a question regarding the outcome of the limma workflow comparing one-colour studies with two-colour common reference studies. I stumbled across the observation...Hello,
I have a question regarding the outcome of the limma workflow comparing one-colour studies with two-colour common reference studies. I stumbled across the observation that the R-squared seems to be in average much …
updated 10.4 years ago • andreas.schuettler
gene expression from some Illumina HT-12 v4 data on GenomeStudio but when I try to follow the limma user guide, I run into errors right at the start when I try to use neqc:
```
x <- read.ilmn(files="Diff Expression Probes.txt...InfY<-neqc
```
I thought maybe I had exported the wrong data from GenomeStudio since the limma user guide says "probe profile.txt" but I only found "Diff. Ex…
updated 3.6 years ago • orbitofrontal
div class="preformatted">Hello,
I've analyzed a time course expt (on affy chips) with limma where
there is
one effect besides time. I've got 2 lists of significant diff
expressed
genes (one for each coefficient
Hi
I am doing some non specific gene filtering prior to DE with limma and I am just wondering when I am filtering based on variance how much filtering I can do and still call my DE results...Hi
I am doing some non specific gene filtering prior to DE with limma and I am just wondering when I am filtering based on variance how much filtering I can do and still call my DE results with...limma 'val…
updated 10.5 years ago • chris86
now is a spreadsheet containing a summary of normalized expression values. I know that for using limma, it is assumed that we have "__eset__" of class "__exprSet__", however, the dataset I downloaded is not definitely of that...class. I need to do DE analysis on that dataset... how can I use limma for this purpose?
I checked these links as well but I did not find an answer for my case:
https://…
updated 10.9 years ago • Momeneh Foroutan
<div class="preformatted">Hi Martha,
What I've done to compare the results of different analyses is to
create a new "TestResults" object combining the output of several
different decideTests:
> results1 <- decideTests(fit1)
> results2 <- decideTests(fit2)
> results3 <- decideTests(fit3)
> results.all <- new("TestResults",cbind(re…
div class="preformatted">
Hello all --
I'm attempting to implement the voom -> limma strategy for the
analysis of a multilevel RNA-Seq experiment with a blocking setup, and
I have a question about how voom...design (taking subject blocking into
account) fed to voom?
An easily accessible example is in the limma users guide, section 8.7,
"Multilevel experiments." Given the target frame …
<div class="preformatted">Dear Dorthe,
The arrayWeights() function does allow you to combine array weights
with spot weights. You are expected to combine the weight analysis
with the most correct design matrix, so including a dye-swap effect
in the design matrix is perfectly appropriate. So, no problems so far.
On the other hand, any spot weight system which removes 70% of your
data is bo…
normalized gene signals (tags per Refseq transcript, length-
normalized) for
each library using the Limma package in R. After Quantile
normalization, we
used Limma to fit a linear model to the log2-transformed data using an
empirical...1.450861588 1.265013193 0.942706046 0.744551693
I'm using the following R-script:
library(limma)
raw.data <-
read.delim("INPUT-QuantileNormalizedLog2Trans…
<div class="preformatted">Dear Jay,
Actually makeContrasts() will recognize an expression or character
string, but it won't always
correctly parse a character-valued variable.
The reason is that makeContrasts() expects to get expressions.
Although it does also allow
character strings to define the expressions, it is too difficult to
correctly distinguish
character vectors from expressions…
to compare B to A and D to C,
but not B to D or B to C, etc.
Do I
1. Run all 4 groups together in Limma and then analyze the individual contrasts
OR
2. do I compare B to A and D to C in 2 separate Limma runs?
I believe that 1 is correct...one should take into account
the variability of all of the samples, Furthermore, as I understand Limma, more
samples improves the empirical Bayesian est…
updated 8.1 years ago • raf4
I'm getting dramatically different results w camera from limma 3.28 vs 3.22 .. the new version gives pvalues <1e-16 while the old one is barely significant on <identical inputs>...I'm getting dramatically different results w camera from limma 3.28 vs 3.22 .. the new version gives pvalues <1e-16 while the old one is barely significant on <identical inputs>.…
<div class="preformatted">At 03:43 PM 10/09/2003, Nolwenn Le Meur wrote:
>... we are using a commmon reference.
>... experiment is:
>
>Cy5Infarctus 5days/Cy3Reference (3 replicated slides)
>Cy5Infarctus 15days/Cy3Reference (3 replicated slides)
>Cy5Infarctus 30days/Cy3Reference (3 replicated slides)
>
>Cy5Infarctus+drug 5days/Cy3Refere…
<div class="preformatted">Hello,
I am trying to get to the bottom of how limma works and was thinking
about what the best way is to compare one level of a variable to
multiple other levels. For example say we had three sample types A, B
and C and I want to find genes that are differentially expressed
between
A and the other samples. I can see that there would be two ways to
set
up the de…
WITHIN arrays, too?
- is there a way to export the normalized single-channel intensities
from
LIMMA?
thank you, any help appreciated.
Federico</div
updated 20.9 years ago • Federico Scossa
<div class="preformatted">In response to a number of requests, I've added a generic import
facility
to read.maimages() in limma.
I've added a new argument 'other.columns' to the read.maimages()
function.
This allows arbitrary columns from the image analysis output files to
be
read into the RGList data object. The columns will be assembled into
data
matrices in the 'other' component of the …
Hi so I'm trying to do limma fitting on my data but i keep getting the following error
<pre>
> library(limma)
> data<-read.table("C:/Users/test/Desktop
updated 11.1 years ago • z.biranvand1983
empty data I have 27003 spots., searching in forum I found
this
suggestion:
Dear Vanessa,
>
> limma always assumes complete print-tip-groups, so the only way to
> use imageplot() correctly is to complete your arrays by
div class="preformatted">Hi Susan:
> Does anyone have experience using limma with 2-color microarray data
> obtained from the Applied Precision SoftWorx Tracker? I can read
the
> .txt files with
updated 20.2 years ago • David Henderson
<div class="preformatted">
Hi all, sorry if I write such a "not strictly technical" question to
this mailing list. Even if not linked to the programming, maybe
somebody would be so nice to comment on my issue.
On a dataset I performed a simple DE analysis between two groups
through limma (eBayes and topTable). The histogram of the p-values are
quite nice, showing a good number DE genes: a…
a design matrix with the argument
ref="Control" I tried to fit above coefficients.
>From limma userguide chapter 9.3 Common Reference Designs it is
suggested to fit the coefficients on RGList object:
fit <- lmFit
processing a set of around 40 Affymetrix hybridizations of (I
think) quit good quality. When I run limma on the rma-normalized set,
everything runs smoothly.
> fit<-lmFit(eset.rma, design)
> fit<-eBayes(fit)
However when
Are repeated measures anova with limma(IE using duplicate correlation and a blocking variable and a measurement covariate) directional? Will it automatically
updated 11.0 years ago • kodream
Recent ...
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