div class="preformatted">Hi all,
When running differential expression analysis on Limma with GDS or GSE
data retrieved with GEOquery, what is the right input option: do.log2
= TRUE or do.log2=FALSE? I read in one
Order by: Relevance
object is utilized here.
Thanks in advance,
Maciej Jo?czyk
> Dear Vanessa,
>
> limma always assumes complete print-tip-groups, so the only way to
> use imageplot() correctly is to complete your arrays by...45 +0200
>>From: Vanessa Vermeirssen <vanessa.vermeirssen ...="" at="">
>>Subject: [BioC] limma printer layout
>>To…
updated 14.2 years ago • Maciej Jończyk
and list,
Could you please explain why the multiple comparison adjustment
procedure implemented in limma (i.e. decideTests) only do adjustment
across genes but not across treatment contrasts within a gene??? I
found one of your...stat.ethz.ch/pipermail/bioconductor/2012-November/049385.html
):
"Post hoc tests are done in limma using decideTests(), and many
options are
offered. You won't find c…
div class="preformatted">Thank you in advance for your help.
We are trying to use limma package to extract and normalize Agilent
2-channel data. Our objective is to use a single 2-channel chip as 2
1-channel...chips.
We attempted the following:
> library(limma)
> targets <- readTargets("targets_file", row.names = "Name")
> RG <- read.maimages(...)
>…
div class="preformatted"> From today (limma version 1.5.1) the development version of limma can
be
run under either R 1.8.1 or R 1.9.0dev. So there is again only one
The data were collected in several batches. We know age and sex of each patient.
Initially I run *limma* using a model
```
~ treatment + day + batch + age_group + sex
```
It shows very strong batch effects. The figure below shows the numbers...and the model is too good to be true. Is there a way of finding if the model overfits data in *limma*?
Note: the input for limma is a matrix …
updated 3.7 years ago • M.Gierlinski
div class="preformatted">Dear members of the Bioconductor mail-list
dear maintainers of the limma and marray packages
I wonder if there is proper handling of the Agilent 44K arrays is
implemented in marray.
Meanwhile...I'm analyzing my human 44K in limma,
and everything works fine with a great help of the list and almost
perfect userguide
(I'm rather biologist, than bioinformatician...Than th…
updated 19.7 years ago • Nataliya Yeremenko
div class="preformatted">Dear Mike,
limma does exactly what you want. The approach outlined in the User's
Guide (and in the workshop)
finds genes which change over...the contrasts, as
long as the contrasts span all the times.
As far as verbosity is concerned, limma is a general purpose program,
not specifically for time
courses. So to create the F-test, you do need to explicitly setup...a…
div class="preformatted">Dear members of the Bioconductor mail-list
dear maintainers of the limma and marray packages
I wonder if there is proper handling of the Agilent 44K arrays is
implemented in marray.
Meanwhile...I'm analyzing my human 44K in limma,
and everything works fine with a great help of the list and almost
perfect userguide
(I'm rather biologist, than bioinformatician...Than th…
preformatted">Hai,
I had few questions regarding the analysis of Agilent microarray data
using the LIMMA pacakge.
Is it possible to analyse the single color data using the
R+Bioconductor
using the LIMMA package? We dont have...of that
we
have pooled the samples before sending for the analysis.
So is it possible to use the LIMMA package without having any
replicates.
--
[[alternat…
updated 13.7 years ago • Muralidharan V
52:39 +0200
> From: "Jakub Orzechowski Westholm" <jakub at="" lcb.uu.se="">
> Subject: [BioC] limma problems
> To: <bioconductor at="" stat.math.ethz.ch="">
>
> Hi! I'm using the limma package to analyze 2^3 factorial experiment
reply. Apologies I should have been a little
more
> descriptive in my problem. I am aware that Limma cannot calculate
any
> statistics without replicates. So I wanted to get the fold change
only using
> topTable, but...of replicates. Can you please guide me how to find out fold
changes
> without replicates using Limma. I am using agilent single channel.
Once again
&…
expression of three cell types to
identify differentially expressed genes. For this purpose, the limma
package seems ideal. However, for one of the analyses, I would like to
focus only on the transcription factors of the cell...types. This
implies
that I only consider about 990 genes. Is this enough to perform an
analysis
with limma, or does it require a larger number of genes at minimum to
give
…
updated 11.6 years ago • Bas van Gestel
<div class="preformatted">dear members,
I have a general question about the creation of design matrices for
non-reference designs in limma.
The set-up of the experiment I'm refering to looks like this:
------------------
0h 1h 2h 4h
3 7 11
A > C > E > G
^ 1…
using a
common reference design.
We are interested in various contrasts between the 8 samples.
Using limma - I was able to generate topTables for the required
contrasts
eg:
A1-B1, A2-B2, A3-B3, A4-B4
A1-A2, A2-A3, B1-B2, B2-B3 and so on
A comparison...A and strain B in the
conditions 1 and 2.
Now when I include the following contrast in my model in limma
(A1+B1)/2 - (A2+B2)/2 which in my under…
At 09:54 PM 1/07/2003, Ramon Diaz wrote:
>Dear Gordon,
>
>Thanks for such a nice package as limma. I just downloaded the latest
version
>(1.1.6) but I noticed that usersguide.pdf is not as updated as
>usersguide.html...releases. The current pdf is up-to-date for the
last
Bioconductor official release, that is for limma 1.0.8.
Gordon
>Best,
>
&…
div class="preformatted">Dear List,
I would like to ask a question about using limma package to compare
multiple groups.
As I understand, if I use multiple testing method "separate", I will
not
have a p-value...to find an
answer
to this question, however I am not sure how to proceed with the
methods
offered by limma package.
Can anybody, please, explain to me how can I perform a procedure
si…
<div class="preformatted">Dear Sally,
Here are two pieces of advice which apply generally to most functions
in Bioconductor or R, and certainly to limma.
Firstly, tuning arguments are usually set to default values which are
sensible for most purposes. You would have to have...two pieces of advice which apply generally to most functions
in Bioconductor or R, and certainly to limma.
Firstl…
updated 18.2 years ago • Gordon Smyth
div class="preformatted">Hello Everyone
I am working through my data using the LIMMA users guide and have a
question
about forming a contrast matrix using a reference design. I have four
samples
in my experiment...B and D.
When designing my contrast matrix my initial thought was to put the
following
command into LIMMA:
>contrast.matrix<-makeContrasts(A-B,C-D,B-D,levels=design)
…
and Feature Extraction from Agilent.
I'm wondering if there's a way to import these data into limma. Out of
the
three required input files (GAL file, Targets file, Spot-type file),
we only
have GAL file. FE gives us SHP file and...expected to have the same result)? And is it possible to give a
set of
probes as normalizing set for limma (set ratio to 1-1)?
I've been looking through the manual bu…
updated 17.6 years ago • Anh Tran
div class="preformatted">Hi,everyone.
I am now analyzing my microarray data using limma. I am not sure
when to use between-array normalization.
In the first case of chapter 11 in limma user's guide, it is
mentioned
updated 18.2 years ago • De-Jian ZHAO
I just couldn't find a function to
transform a simple data.frame with microarray log2-ratios into a
limma-type ot marray-type objects.
I have a data.frame containing (R/G-) log2-ratios for the each slide
in
a separate column and...I 'd like to use some of the functions available
in limma or marray, in particular to run a lowess normalization. I
realized that I need either limma or marray specif…
updated 18.1 years ago • Wolfgang Raffelsberger
35:41 +0100
>> From: Yannick Wurm <yannick.wurm at="" unil.ch="">
>> Subject: [BioC] of limma and superfluous arrays
>> To: bioconductor at stat.math.ethz.ch
>>
>> Dear List,
>>
>> I'm starting to do...US22502600_F83_S01.gpr F_24h Ref
>> ... and six more
>>…
updated 17.9 years ago • Yannick Wurm
in the data,
then Rank Products does well as its difficult to estimate the true
mean
or variance. Limma does better than classical statistical methods as
it
uses a moderated variance estimate.
However as the data improves...statistical tests that utilize both mean and variance
estimate
do better than Rank Products. Limma also performs well in this case.
Overall, we recommended limma as it perfo…
div class="preformatted">Hello all,
I am using limma on Affymetrix data and I read and followed the User's
Guide
so far, ?but one thing is still not clear to me:
Are the M-Values
the effect on gene expression levels of two
factors Age
and activity (each with 4 levels) using Limma.
for my design matrix i have
dataB<-data.frame(samples = arrays,Age=factor(FFAge),activity =
factor(FFfibrosis))
design
can I import normalised M and A values from other
program and then perform linear model fit using limma.
==============================
Binita Dutta, PhD
MicroArray Facility(MAF)
UZ Gasthuisberg
Onderwijs en Navorsing
Herestraat 49
3000 Leuven
Belgium
<div class="preformatted">Dear Bioconductors,
I am wondering whether it makes sense to use genes with log odds less
than 0
generated from Limma. There are only a handful of genes with B>0. I
observe
the volcano plot of log odds vs. log ratios, and it seems to me that
even...I am wondering whether it makes sense to use genes with log odds less
than 0
generated from Limma. There are o…
Hello,
I am happy to see that Limma is updated to handle RNA-Seq data. I have FPKM values for my transcripts. Can I use them directly as input to Limma? Is there...any kind of normalization to do on FPKM values prior to using Limma?
Thanks,
Delasa
updated 10.8 years ago • Delasa Aghamirzaie
div class="preformatted">Hello limma users/developers,
Are missing values imputed in limma, and if so, which imputing method
is
used?
Thank you.
--------
Yiwen He, Ph.D
w/o
inhibitor). After manual normalization based on control spots on each
membrane, I like to run limma as factorial design. My question is how
I
should handle the duplicate spots (block effect) in limma processing?
Thanks
updated 20.6 years ago • Jianping Jin
subsetting etc. This ended up being very laborious,
and
there may not be a way to do this easily in limma, but I could be
missing something.
What I have is this: 4 treatments: A,B,C,D
For each treatment, I have 2 technical replicates...dye swaps), I want
to average these in limma, and then look at comparisons between
groups,
and create contrasts between A and B, etc. However, I dont see an easy
…
<div class="preformatted"> Dear List,
I have been trying to use limma to identify differentially expressed
genes
but have been finding some difilcuties in creating a basic
model.matrix. and
establishing a contrast. I usually have two different types of RNA in
triplicates, a reference an an experimental and wish to see genes
differentially expressed between the them. Following the limma man…
div class="preformatted">Hello Everyone,
I have encountered an unexpected behaviour in limma vennDiagram
function and
I am unsure whether that is the intended behaviour and if so, what the
interpretation is.
Here...loaded via a namespace (and not attached):
[1] tools_2.12.0
I have analysed my data using limma and then I got whether the related
t-statistics are up, down or not significant fo…
15 Aug 2005 15:30:34 -0700 (PDT)
>From: Wenbin Liu <wnbnl at="" yahoo.com="">
>Subject: [BioC] limma and block effect
>To: bioconductor at stat.math.ethz.ch
>
>Dear limma users,
>
>I have an experiment designed
<div class="preformatted">Hi,
I've been using the limma normalizeBetweenArrays function to
perform cyclic loess normalisation on single channel microarray data
(non-log...div class="preformatted">Hi,
I've been using the limma normalizeBetweenArrays function to
perform cyclic loess normalisation on single channel microarray data
(non...intensities, and so any advice/insights
would…
updated 12.0 years ago • MIKE STARKEY
div class="preformatted">Dear list,
I have a question regarding to nonspecific filtering prior to limma
analysis. I've searched on google, but no answer.
I have a microarray experiment with three groups: group1, group2 and
group3.According...to limma vignette, my analysis would be like this:
f<-factor(targets$Target, levels=c("group1","group2","group3")
design<-model.matrix...c…
updated 16.1 years ago • Javier Pérez Florido
<div class="preformatted">Dear Gildas,
Yes, I agree, thanks for pointing out the problem. I have committed a
fix
to the package.
The older code in limma 2.18.2 was slower but correct. The later code
was
fast but didn't treat NAs correctly. The code should now be both fast
and...thanks for pointing out the problem. I have committed a
fix
to the package.
The older code in limma 2.18.2 …
GoldenGate Methylation Cancer Panel I. For each spot,
there are a p-value for quility. I want to use limma to analysis the
data. How can I set the quility weight for each spot? From the manual
of limma, it can be set by read.maimages
div class="preformatted">Hi
I have a very basic question about limma.
Assume I have experiments from 3 or more RNA sources in a reference
design.
It is easy to define individual contrasts
<div class="preformatted">Hi,
I am using limma for a variety of projects. It all seems pretty
straightforward for projects where I am not as concerned with the
interaction of the independent variables,
but I am a bit confused on how to create the contrasts so that I can
focus the analysis on the interactions between the independent
variables. I have read the users' guides and vignettes an…
<div class="preformatted">All,
In section 8.6.2 of the limma user's guide, an example is given using
splines for time-course data. It looks like in this example, the data
points are independent...div class="preformatted">All,
In section 8.6.2 of the limma user's guide, an example is given using
splines for time-course data. It looks like in this example, the data
points are...function …
<div class="preformatted">
Hi all,
I am just wondering how to process replicate genes in an array using
limma package. each gene is printed twice on an array.
For example, the actual number of genes is 19000 in my dataset, since
there are replicate genes, I have 38400 spots (genes) in my dataset.
I am just wondering how I can get 19000 genes from these 38400 genes
before or after normal…
Gordon
>
>I am sorry if I made any incovinience. I have a question about design
matrix
>in limma.
>We've designed experiment and completed. But it's pretty tough to
analysis.
>Design is 2 x 2 x 2 factorial design and...This raises a lot of issues of which probably the easiest is how to
create
a design matrix in limma. Let's consider the design matrix first.
You…
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
>
Hi ingunn & all
…
data collected with Affymetrix MouseGene 2.0
ST chips. I have a few questions about properly using limma. I have
four groups with three replicates. The groups are Control, Treatment
#1 & #2, Treatment #1, and Treatment #2. I may not...use in linear regression.
Currently, my design matrix is set up like this:
# Design matrix for Limma
design <- model.matrix(~ 0+factor(c(1,1,1,2,2…
updated 11.9 years ago • Matthew Thornton
<div class="preformatted">Hello, all.
I have a time course with six time points at 3-5 replicates per time
point
(total of 23 Affymetrix GeneChips). I would like to use limma to do
comparisons between time points. I would like to normalize everything
(all
18,000 probesets) with RMA, but then only examine the 180 genes
involved in
ion transport. These are custom affy chips, and not sufficie…
dat.m))
rn<-rownames(tt)[tt$P.Value<-0.001]
I got only 127 genes
But i dont know how to work limma package, In my folder have four CEL
files.
How to limma know about wild type and mutant cel files and how
compare, that
i want
<div class="preformatted">Dear Hatice,
Thanks for your question about recent updates to the limma package.
You
can see a description of all recent changes to the package by typing
changeLog(100)
at the R prompt, where the...div class="preformatted">Dear Hatice,
Thanks for your question about recent updates to the limma package.
You
can see a description of all recent changes to th…
<div class="preformatted">Dear all,
I have a problem with the log Fold changes calculated in Limma. I am
using protein abundance index of proteomic data
The log2 of this data is normally distributed and after log2, I use...div class="preformatted">Dear all,
I have a problem with the log Fold changes calculated in Limma. I am
using protein abundance index of proteomic data
The log2 of thi…
div class="preformatted">
I use Limma Dev. Package and i'd like output my normalized data, but i
have a problem:
> library(limma)
> library(sma)
>YourSample<
a design matrix? Why not
design <- modelMatrix(targets, ref="C")
as described in the limma User's Guide?
Best wishes
Gordon
> Date: Tue, 15 Mar 2011 14:52:05 -0400
> From: Luis Z <luisgls at="" gmail.com="">
> To: bioconductor...at r-project.org
> Subject: [BioC] limma design experiment
> Message-ID:
>
> Hi everyone,
>
&…
time in several years,
I've
made a user visible change to the empirical Bayes procedure used in
the
limma package. I have changed the hyperparameter estimation to make it
less
sensitive to sample standard deviations which...more stable results.
I've committed the new version to the developmental version of
Bioconductor
as limma 2.4.0. I'd be pleased to receive feedback if there are
problems.
Fur…
div class="preformatted">Hi List
When using duplicateCorrelation in Limma running under Linux I am
receiving the following error:
> cor <- duplicateCorrelation(MA, design=design, ndups=2,
weights...Lapack
routine 'dgesdd'
Interestingly, there are no problems when analysing the same dataset
in Limma running under Windows indicating a problem with the Linux
version/installation.…
div class="preformatted">I am using limma normalizeWithinArrays with method
="robustspline" and other default settings. I got the
following warning: rlm failed
div class="preformatted">hi everyone,
I have some problems with exporting data with limma, i carried out
background correct process with my two color array, after that, i want
to
export the processing expression
impute, but my n is not huge and consists of four non-distinct
groups). My
question is:
How does limma handle missing data? It doesn't mind NA's coming in,
but
does it correct for the different df at each gene given the number
div class="preformatted">Hi,
-using Bioconductor v1.8.1 and limma v1.6.1
When I use backgroundCorrect(minimum) and then dupcor.series I don't
get
a correlation value (NaN), if I don't use...statmod
Attaching package 'statmod':
The following object(s) are masked from package:limma :
matvec vecmat
> cor$cor
[1] NaN
> MAdef=normalizeWithinArrays(RG, RG$printer)…
analysis program? And how
can I can remove these bad spots from further calculation in R using
the limma package or any other functions in R?
Thanks,
Anna</div
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