in a way that is not compatible with that language. If I'm
right,
it's an R issue rather than a limma issue.
You could clarify this by giving us system information:
sessionInfo()
There are a number of previous posts on these...at="" hotmail.com="">
> To: <bioconductor at="" stat.math.ethz.ch="">
> Subject: [BioC] LIMMA
>
> I have a problem when running …
Order by: Relevance
div class="preformatted">Hi,
I am trying to read in cDNA spotted microarray data into limma.
I would like to check for spatial heterogeneity in the samples and
therefore I would like to define the printer layout...code completely, so you have an idea of what I have read
in already.
#reading cDNA spotted arrays in Limma Bioconductor package
library(limma)
targets_e1a <- readTargets()
RG…
updated 18.3 years ago • Vanessa Vermeirssen
div class="preformatted">Hi,
I'm new to the mailing list and to R/limma so please be gentle.
I found a previous posting (Sept. 2007 - 'different gal files using
limma') on how to deal with two gal files...in limma but is it possible
to
handle > 2 gal files?
In short, can you cbind(MA1, MA2, MA3) ?
Regards,
Mark
******************************************
Dr Mark Alston,
Computational
div class="preformatted">Dear List,
I have been thinking with using limma package to perform some time
series
analysis. There is a simple example in limma's manual. However, it
seems that
the analysis...the manual does not consider the repeated measurement
effect for
time series data.
I am wondering if limma has developed any method to deal with such
time series
data. Or I have to manually ad…
2008 22:35:41 +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 limma analyses...Ref
> US22502600_F83_S01.gpr F_24h Ref
> ... and six more
>
>For my limma analysis, …
updated 17.9 years ago • Gordon Smyth
cDNA microarray data. As I need a spatial
>normalization, I will try to do it before the use of limma package.
Remember that print-tip-loess is in itself a simple form of spatial
normalization (as well as intensity-based...But, as you say, if you really do want to do formal 2D normalization
you'll
have to do it outside of limma.
>I am also running a Genechip experiment, with four …
updated 22.4 years ago • Gordon Smyth
Dear Bobby,
I've tried the code you give below on a GenePix gpr file, and it works
fine in limma 2.7.9. So
the problem does not appear to be a change in limma.
I assume that when you run the code that "B635 Median" is on one...gt; From: Bobby Prill <rprill at="" jhu.edu="">
> Subject: [BioC] readGenericHeader problem in limma 2.7.8?
> To: bioconductor at stat.math.ethz.ch
&…
Dear Communities
As the author of limma suggested, the DEG analysis of RSEM expected count should be done by limma::voom from a computational point of view (https...2000 genes when the Ensembl ID was transformed to the official gene symbol. So I wonder whether limma::avereps could/should be conducted to remove duplicated genes before feeding to voom. Any suggestions would be great...appreciati…
lmFit() are correct for this
single error component approach.
I am sorry that the theory behind the limma approach to technical reps
has not yet been written up
and published. I am trying to find time to do this. The theory is...50 -0400
> From: Naomi Altman <naomi at="" stat.psu.edu="">
> Subject: [BioC] technical reps, limma - theory
> To: bioconductor at stat.math…
div class="preformatted">Dear List,
I'm starting to do limma analyses on a small timecourse loop design
with 2-color cDNA chips as follows:
0h vs 6h
6h vs 24h
24h vs 0h
Four biological...A_24h Ref
US22502600_F83_S01.gpr F_24h Ref
... and six more
For my limma analysis, I have three options:
*a*: use only the minimal number of chips (ie eac…
updated 17.9 years ago • Yannick Wurm
on checking back through the records, I can see that none of
the
Bioconductor
release versions of limma would have given the below error. You must
be
using an
in-between version of limma from between Feb 8 and March 20 of this...gt;From: Gordon Smyth <smyth@wehi.edu.au>
>Subject: Re: [BioC] Problem with gls.series in limma
>Cc: bioconductor@stat.math.ethz.ch
>
>Y…
update of bioconductor it appears to me that a little
bug has
been introduced into plotMA() in the limma package:
Selecting the desired array with plotMA(foo, array=2) does not work
anymore if foo is an RGList.
The reason seems...in the respective part of the
source code
from
MA <- MA.RG(MA[, array])
array <- 1
in limma 2.12.0 (2007/09/25)
to
array <- 1
MA &l…
div class="preformatted">Hi,
I have a simple question about using limma to analyse gene expression
data form a custom microarray with over 180k probes. The probes were
designed to include...gene ABC will be mostly alike in the
direction of differential expression. I was wondering whether limma
analysis of such data will lead to erroneous estimates of probe and
significance effects? Is limma …
updated 14.3 years ago • Max Mariasegaram
52 -0700 (PDT)
> From: yuhong ning <yhning at="" yahoo.com="">
> Subject: [BioC] log2 ratio as limma input
> To: bioconductor at stat.math.ethz.ch
> Content-Type: text/plain; charset=iso-8859-1
>
> Hi,
>
> I am trying...to use limma to analyze Mass Spec data for
> differentially expressed proteins from wild type cell
> an…
gt;Date: Tue, 20 Sep 2005 10:55:19 -0500
>From: <yjzhang at="" uiuc.edu="">
>Subject: [BioC] limma normalization warning
>To: bioconductor at stat.math.ethz.ch
>
>I am using limma normalizeWithinArrays with
updated 20.3 years ago • Gordon Smyth
Can I ask - I understand that Limma - Voom has been created for RNA -seq --> do you know if it is suitable to be used for micro arrays as well, since LIMMA was created
updated 4.3 years ago • jonathan_paul
div class="preformatted">I am using the limma application and am wondering whether there are is
a
QualityWeights function available for Imagene? If not, is there
div class="preformatted">Dear Michael,
limma expects spots to be in "standard order", in which the fastest
to slowest moving indices are spot columns, spot rows, grid...53 +0100
>From: "michael baron \(IAH-P\)" <michael.baron at="" bbsrc.ac.uk="">
>Subject: [BioC] limma and print tip groups
>To: <bioconductor at="" stat.math.ethz.ch="">
>Message-ID:
&am…
updated 19.3 years ago • Gordon Smyth
div class="preformatted">
I have been using limma for a little while, for the analysis of
2-colour cDNA arrays.
I am going to get pretty soon some data from Nimblegen. This...I thought that 'affy' would be the way to go, but since it's
a 2-colour hyb, I suppose that 'limma' could handle it. In fact, from
limma I could choose to treat the data as single channel arrays if I
had to, and I am alr…
experimental more than two and a half years ago, when the
function were first introduced into the limma package. I've done much
more testing since then, and the function has stood the test of time,
so I'll remove the warning.
Best...wishes
Gordon
>[BioC] limma help - choosing an approach
>john seers (IFR) john.seers at bbsrc.ac.uk
>Thu Sep 14 12:19:39 CEST 2006
>
&am…
div class="preformatted">Hello
Dear all
I have a question about topTable in limma package. Can i specify
parameters of interest in
topTable, i.e. it gives me specific parameters such as adj.P-value
and...of them are caused to disorder output file of
topTable. I would like to
process our data in excel
limma(library)
targets=readTargets("ApoAITargets.txt")
RG=read…
from a variant of RNA-seq which I am hoping do some
moderated t-test differential testing on with limma. In this data,
many of the reads have sequenced through into the poly(A) tail, and we
believe this gives us information about...error is low.
What I'm hoping is that this can be translated into weights that can
be fed to limma to make it behave correctly. Do weights have some
specific meaning …
09:06:20 +0200
> From: "Jakob Hedegaard" <jakob.hedegaard agrsci.dk="" at="">
> Subject: [BioC] Limma - error when using duplicateCorrelation
> To: <bioconductor at="" stat.math.ethz.ch="">
>
> Hi List
>
> When using duplicateCorrelation...in Limma I am receiving the
following error:
>
>> cor <- duplicateCorr…
<div class="preformatted">Hi,
please apologize my ignorance, but:
I have the impression that limma is calculating the means
of M values by averaging them after adjusting the signs of the
values to the design matrix.
But...div class="preformatted">Hi,
please apologize my ignorance, but:
I have the impression that limma is calculating the means
of M values by averaging them after adjust…
div class="preformatted">Dear Hong,
You can fit any multiple regression model in limma, so the issue isn't
one
of software but rather of deciding what model you want to fit. And we
can't tell you that. One possibility...gt; To: "bioconductor at r-project.org" <bioconductor at="" r-project.org="">
> Subject: [BioC] limma: multiple regression
>
> Hello all,?
&g…
updated 14.6 years ago • Gordon Smyth
div class="preformatted">Dear all,
the limma documentation stored here:
http://www.bioconductor.org/packages/2.3/bioc/manuals/limma/man/limma.
pd
f
has some lines
div class="preformatted">
Dear List,
I think I know how to do this with limma.
I first calculate the correlation treating each strain as a block
block<-rep(1:3,c(4,3,2))
biocor<-duplicateCorrelation...3 technical
replicates. In order to simply the anlaysis, I just average the
replicates and then use limma to do the job.
How could I include such technical replicate information a…
with colnames which look like the
followings. I am wondering how to proceed with this data by using
limma to do the QC. I mean, I probably can create some corresponding
objects of limma manually (like RGList from gMedianSignal
div class="preformatted">Dear Mark,
The short answer is that limma always assumes a common gal file for
all
arrays, so there are no automatic ways to handle two or more gal
files.
It is sometimes...IFR\)" <mark.alston at="" bbsrc.ac.uk="">
> Subject: [BioC] handling multiple gal files in limma
> To: <bioconductor at="" stat.math.ethz.ch="">
> Content-Type: te…
<div class="preformatted">Hi
Consider the design matrix in the limma user guide, section 10.7:
FileName Strain Treatment
File1 WT U
File2 WT S
File3 Mu U
File4 Mu S
File5 Mu S
Does it matter if...div class="preformatted">Hi
Consider the design matrix in the limma user guide, section 10.7:
FileName Strain Treatment
File1 WT U
…
are
not logarithmized signals.
My question is how should I proceed with the data if I want to use
limma to
analyse it? Or should I use the original CEL files and a standard
approach
(as described, for example, in the limma guide...If I dumbly run limma, I am getting more or less the results I expect,
but
the p-values seem to me overly optimistic:
g2 <- new( "EList", list( targets
<div class="preformatted">
> Date: Mon, 2 Jun 2008 15:26:20 -0700
> From: "Anh Tran" <popophobia at="" gmail.com="">
> Subject: [BioC] Using limma with Agilent array data
> To: "bioconductor at stat.math.ethz.ch" <bioconductor at="" stat.math.ethz.ch="">
>
> Hi all,
>...2008 15:26:20 -0700
> From: "Anh Tran" <popophobia …
updated 17.6 years ago • Gordon Smyth
each time point. We used gcrma to
pre-process and normalize our expression data.
We want to use Limma to analyze differential expression in this time
course experiment. We have limma 1.8.22 that we run on a Windows XP
system...We have tried to follow the example on page 36 of the limma
user's guide, but we seem to have difficulty executing some of the
procedures. For example the contrastMatr…
div class="preformatted">How does the method "fdr" in limma work? Strictly speaking, I am not
aware that fdr methods actually adjust p values but rather set p value
cut-offs according...cut-off would be expected to have a false positive rate
of
the value q.
I have played around with limma's fdr method a bit and I get the
feeling
that, after fdr correction using p.adjust, perhaps I should set …
div class="preformatted">Without hacking into the code behind LIMMA, is there a way to perform
partial F-tests for groups of variables outside of creating
complicated
contrast matrices...It should be obvious that this is best
attacked
using a partial F, but how to implement this in LIMMA??
Thanks!!
Dave H
PS I'm in digest mode and will reply when I receive the digest.
Alternatively cc me on…
Dear Bioconductors,
I have a problem defining a contrast using the function makeContrasts
in LIMMA. It seems to me as if my problem has to do with the way the
function deals with groups with names that contain digits and...groups,
therefor I would be very grateful for a hint how to deal with these
group names.
I am using limma 2.0.7 and R 2.1.0
Thanks a lot!
Georg
</div
stage.
limmaGUI provides plenty of facilities to do this, but if you export
the data out of the limma to treat it using other tools, then
obviously this becomes your responsibility.
BTW, limmaGUI provides features for...33 -0700
>From: "Adrian Steward" <adrian.steward0405 at="" gmail.com="">
>Subject: Re: [BioC] limma: print-tip loess and empty spots
>To: keith at wehi…
updated 18.6 years ago • Gordon Smyth
class="preformatted">The normexp likelihood is difficult to compute with full numerical
accuracy. In limma version 2.3.1, I made what I thought was a slight
improvement in the likelihood calculation, which has instead had the...to extreme parameter values, producing the effect
that you see.
I believe the problem is fixed in limma 2.4.5 and later. Try upgrading
and see.
Best wishes
Gordon
&a…
updated 19.9 years ago • Gordon Smyth
<div class="preformatted">Dear list,
when using read.maimages from limma with a "broken" file (tabs
replaced
by ":", two extra tabs added at the end of row e)
limma reads the table fine
table:
:R:G:RB:GB
a:1:2:0.5:0.5
b:2:4:1:1
c:3:6:1.5:1.5
d:4:8:2:2
e:5:10:2.5:2.5::
f:6:12:3:3
g:7:14:3.5:3.5
code:
RG<-read.maimages(files="test.txt",
path="C://cpan//",columns=list(Gf="G",
…
10:37:42 +0200
> From: Matja? Hren <matjaz.hren at="" nib.si="">
> Subject: [BioC] Weights in limma package (theoretical question)
> To: <bioconductor at="" stat.math.ethz.ch="">
>
> To all users of limma,
>
> We are using...limma package for differential gene expression
analysis. We also use weights (0 and
> 1) based on quality …
that fail the null hypothesis that they are
all
the same across >2 treatment groups using the limma package (which I
find exceptionally useful, by the way).
If I were doing this for a single gene, I'd use a traditional F test...limma's eBayes generates an F value (via classifyTestsF) from the
individual t statistics, but if I use a model without an intercept...belo) but
finding that is pr…
div class="preformatted">I'm reading smd file into limma and would like to give weight of zero
to
spots with FLAG != 0 (-50 in my file). I type the following:
* RG<-read.maimages("/home/jstraubh
1
what does Warning message mean here? and why corfit$consensus is -1?
I used R version 2.0.0 and limma version 1.8.12, then I upgraded limma
to version 1.9.0, and I got
same Warning message from each version of limma.
Any help
treated_mice _9 untreated_mice_9
array_10 untreated_mice_10 treated_mice _10
Usually I use LIMMA package to perform statistical analysis but I
looked LIMMA userguide up not finding anything...
Does someone knows if...LIMMA supports this experimental design?
How do I have to consider (biological replicates, etc.) the
arrays?...I think they are indipendent
updated 17.3 years ago • Erika Melissari
a bit back through the archives and couldn't see an answer
to this, so perhaps someone can help.
Limma uses a Printer Class to identify which print group a spot
belongs to. This data object includes the number of grids, their...the spots in the first row across
the ARRAY first, then the second row of the array, and so on). Is
limma expecting the data to be 1st row of 1st grid, then 2nd row of
1s…
<div class="preformatted">Dear list,
I am working with Affymetrix microarrays and looking for differential
gene expression using limma. We repeated the same microarray
experiment
two separate times (about a year apart), because *some* of the
microarrays came out bad. So instead of running the same samples
again
(technical replicates), we generated an entirely new set of RNA.
(i.e. for tre…
<div class="preformatted">Hello,
I have Illumina 450k methylation data sets for 20 males (10 cases and
10 controls) and 20 females (10 cases and 10 controls), which I have
been analyzing separately using MINFI and LIMMA. The phenotype that
defines the cases and controls is the same for both data sets. Is
there any way to combine both data sets into one and analyze
differential methylation u…
the fastq file (or binary fastq.tbz), could
we use it as input for Voom, and then
use the result for Limma? Or should we align first our raw fastq data
and then use the sam or bam files as
input for the Vomm or Limma packages? How
div class="preformatted">Hi,
We are trying to use Limma code for a Time Course Experiment without
Replicates for 4 times. From looking at the manual, looks like don't
Need replicates...But the ebayes routine complains about no residual
Degrees of freedom.
Can we use Limma for Time Course without replicates?
Lana
</div
<div class="preformatted">Dear all
When working with comparative experiment based on Affymetrix gene
expression arrays I usually apply one of the following combination of
methods:
RMA + limma + FDR
or
RMA+ Rank Products
(rank products "Percentage of false prediction" values are supposed to
be equivalent to FDR)
Usually we obtain much more differentially expressed genes when using
Rank …
Hi! I'm new to Bioc, and I'm trying to install some packages. I'm having this error whith the limma package:
> biocLite('limma')
BioC\_mirror: https://bioconductor.org
Using Bioconductor 3.5 (BiocInstaller 1.25.3), R 3.4.0..._compilation
limma 3.31.21 3.31.22 FALSE
installing the source package ‘limma’
probando l…
updated 8.7 years ago • segador67
div class="preformatted">Hello limma users.
Can LIMMA fit a linear model to a Poisson distribution?
My dataset is equivalent to an array but instead of intensities
<div class="preformatted">Dear list,
I performed a 9 array Affymetrix microarray experiment with three
genotypes and three replicates of each. I am trying to do GCRMA
normalization, filtering based on MAS5 calls, and then use limma with
contrasts (and BH to adjust the p-values) to identify differentially
expressed genes. I have no problems with the normalization and
filtering, but I am h…
updated 16.0 years ago • Matthew Willmann
<div class="preformatted">Dear list,
I performed a 9 array Affymetrix microarray experiment with three
genotypes and three replicates of each. I am trying to do GCRMA
normalization, filtering based on MAS5 calls, and then use limma with
contrasts (and BH to adjust the p-values) to identify differentially
expressed genes. I have no problems with the normalization and
filtering, but I am h…
updated 16.0 years ago • Matthew Willmann
<div class="preformatted">Hi,
In Chapter 8.1.2 in Limma users guide there is a description how to
detecting the Dye effect.
The example there describes an experiment of Wt vs...div class="preformatted">Hi,
In Chapter 8.1.2 in Limma users guide there is a description how to
detecting the Dye effect.
The example there describes an experiment of Wt...The second option of dye swap preparatio…
and healthy. I can get the contrasts between healthy and disease
comparisons using contrasts in LIMMA. But here each disease has 2-3
arrays from different patient blood samples. These are not true
replicates, per se but thats...all we have. My question is how do we
treat them? Can I consider them as replicates? (I understand LIMMA
will
combine the replicate data.)
here is the design........
1. di…
wrote:
> Dear Ulrike and Henrique,
>
> The problem is more likely to be with the limma normexp.fit()
function than
> with optim().
>
> There is a rare numerical instability which causes an error like
this...with
> normexp background correction in limma 2.14.X. Jeremy Silver and I
did a
> lot of work on this late last year, and we think we …
It is the
simplest
possible microarray experimental design, and is covered in Section
8.1.2
of the limma User's Guide.
> Date: Fri, 26 Sep 2008 18:24:23 +0200
> From: "Erika Melissari" <erika.melissari at="" bioclinica.unipi.it="">
>...Subject: [BioC] Balanced Block design in LIMMA
> To: <bioconductor at="" stat.math.ethz.ch="">, "Gordon K Smyth"
> …
updated 17.3 years ago • Gordon Smyth
<div class="preformatted">Dear Julien,
The component 'Amean' in the output from lmFit() is supposed to hold
the mean log-intensity for each probe, an indicator of the overall
expression level of the corresponding transcript.
However, if the data values input to lmFit() are log-ratios rather
than log-intensities, then there is no way to compute the mean
log-intensities. If the first argume…
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