04:31 -0400
> From: "Lance E. Palmer" <lance.palmer at="" stonybrook.edu="">
> Subject: [BioC] LIMMA P-value calculations/Suggestions for flagged
> data
> To: bioconductor at stat.math.ethz.ch
>
> I just had a question...concern about P value calculations in Limma (I
am
> using latest version of Bioconductor)
>
> I recentl…
Order by: Relevance
I've had several requests for references to published papers in the
biology
literature using the limma package. There have been three articles
appear
since June that I know of:
Golden, T., R., and Melov, S. (2004). Microarray analysis
updated 21.4 years ago • Gordon Smyth
div class="preformatted">Dear all,
I am using limma for the analysis of a factorial experiment for the
first time.
I would greatly appreciate your help re to few questions
<div class="preformatted">Hi,
I have been trying to fit a contrast matrix in Limma using the
'contrasts.fit' function but I keep getting an error:
Error in La.chol(crossprod(design)) : the leading minor of...div class="preformatted">Hi,
I have been trying to fit a contrast matrix in Limma using the
'contrasts.fit' function but I keep getting an error:
Error in La.chol(crossprod(desig…
div class="preformatted">Hi,
in the limma guide, there are several different examples which are
well
described. However, there are two different functions for
updated 21.9 years ago • Simon Melov
<div class="preformatted">I have an experimental design (or rather question) that goes beyond my
usual limma knowledge. I am hoping there is some elegant way to answer
it that someone here can point me towards. The experimental design is
straightforward: one control group (Ctrl) and two treatment groups (T1
&
T2) with three replicates each:
S1 Ctrl
S2 Ctrl
S3 Ctrl
S4 T1
S5 T1
…
Hi
I'm using the limma package to obtain some linear models out of some arrays.
I have the transcription rate of the cell at 7 different growth...Hi
I'm using the limma package to obtain some linear models out of some arrays.
I have the transcription rate of the cell at 7 different growth rates (7 different arrays).
I did created the design matrix, and because I just want the linear model an…
Illumia GenomeStudio-Methylation software.
My question is how can I extract data files required by LIMMA?
I hope to genotype the differential loci indicated by the discovery
array in
a larger sample, and perform association...analysis between methylation
status
or degree with quantitative or qualitative phenotypes. LIMMA is no
doubt the
right tooll to do this.
However, we got problems in transfer…
To: bioconductor
Sent: 6/14/2004 9:44 AM
Subject: [BioC] How to put out the normalization result of limma as a
*.txt
file?
Hello everyone!
I am looking for methods to put out the normalization result. I used
limma to do the normalization
updated 21.6 years ago • Sean Davis
gt; To: Lana Schaffer; Naomi Altman; bioconductor at stat.math.ethz.ch
>> Subject: Re: [BioC] Limma -time course - no replicates
>>
>> You can use LIMMA. The key is to have time be a continuous
variable,
>> not a factor...PM
>>> To: Lana Schaffer; bioconductor at stat.math.ethz.ch
>>> Subject: Re: […
updated 15.4 years ago • Yair Benita
div class="preformatted">Hi,
In Limma I run topTable for Affy chips. After write.table(), there are
8
columns of data, but only 7 headers (and they are misplaced
islands for each of the n = 59 subjects (the dimension of the matrix is roughly 15,000 x 59). The \`limma::lmFit\` method (and related functions) are then used, along with an appropriate design matrix, to assess any evidence of...for bounded outcomes) is preventing any potential signal in the data from being picked up. Does Limma </span>accommodate such analyses, or are th…
<div class="preformatted">Hi,
I have a question about the function avereps in the limma package.
When I compare the relative outputs of this function in limma.2.18.2
and
in the last version limma.3.6.6, I...div class="preformatted">Hi,
I have a question about the function avereps in the limma package.
When I compare the relative outputs of this function in limma.2.18.2
and
in the last …
have one:(
>But hopefully I'm improving...
>
>My mistakes were -
>1.I mixed up lmFit(limma) with lm.fit(stats) - sorry, 1 character's
not
>alot when you are in a hurry;)
>
>2.Being unsure of how lmFit handles factor...c(1,2,3..) vs numeric
>c(1,2,3..) and thinking this example in the Limma user guide meant
-ve
>numbers could be confus…
updated 21.4 years ago • Gordon Smyth
effect 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
Diet.disease
I'm trying to reproduce an old analysis I did using the bioc package limma. I've cloned the [git repo](https://git.bioconductor.org/packages/limma) and I do see limma versions that are part of bioc...I also don't see these versions in the [cran archive](https://cran.r-project.org/src/contrib/Archive/limma/). And google hasn't produced any other leads.
Does someone know how I can download these…
for any assistance. I am having difficulites
with creating a contrast matrix for my data in limma, as well as then
applying the matrix to the modeled data to compute statistics, and the
output for such.
I have included...I was attempting to follow the
tutorial "single channel analysis of agilent microarray data with
limma" by the mattick lab. Unfortunelty mine is not a simple 2x2
factorial mat…
updated 13.8 years ago • Guest User
There's a duplicated word in the current limma userguide.pdf ('last revised 14 Nov 2021'), page 34:
```
(...)and Affymetrix arrays, include include con-
trol probes (...)
```
Btw this manual
updated 3.2 years ago • jeltje.van.baren
2005 15:19:55 +0100
>From: Pie Muller <pie.muller at="" liverpool.ac.uk="">
>Subject: [BioC] Limma and Block Effects
>To: bioconductor at stat.math.ethz.ch
>
>Hi Bioconductors
>
>I followed the example 10.2...in Limma's user guide which includes a
>coefficient for each mouse in the linear model to account for
technical
>replicat…
updated 20.3 years ago • Gordon Smyth
<div class="preformatted">Dear Limma users,
In our study we would like to identify tissue specific genes, i.e.,
genes that are differentially
expressed in a...div class="preformatted">Dear Limma users,
In our study we would like to identify tissue specific genes, i.e.,
genes that are differentially
expressed in...relative LP contribution in
LER)+0.6(M2)+1.2(M5)+0(M7)+1(Trichom)+3(AB)+2(A…
B over A.
Thus far, I have read the data using the beadarray package, and tried
to
follow the limma manual's instructions for paired tests. I am,
however,
unsure about the contrasts, and my results look weird to me.
I have...BSData.genes) < 0.05, 1, any)
BSData.filt = BSData.genes[expressed,]
# set up paired tests using limma - what's wrong here?
library(limma)
patients = c(17, 2, 18, 5…
updated 14.7 years ago • Moritz Kebschull
without error
when i try to use affylmGUI to draw a MA plot,i select use Gene
Symbol,but limma told me Gene Symbol is not avialable.why this problem
would occur?
is there any solution to fix that?Thanks!
here is my...matchprobes
Loading required package: splines
> library(affylmGUI)
Loading required package: limma
Loading required package: tcltk
Loading Tcl/Tk interface ... done
To begin…
div class="preformatted">Hi, All,
I'm doing the analysis on my cDNA array with limma. There are
irregular
replicates for each spot and the spacing numbers are unknown. I'm
trying
to correlate the replicates
<div class="preformatted">> Date: Thu, 1 Jun 2006 11:38:02 +0100
> From: "michael watson \(IAH-C\)" <michael.watson at="" bbsrc.ac.uk="">
> Subject: [BioC] Limma, dye-swaps and uneven numbers of replicate
> arrays
> To: <bioconductor at="" stat.math.ethz.ch="">
>
> Hi
>
> A simple question...0100
> From:…
To
do
this, I have normalized the data in several different ways and
genereated
DEG lists with limma and decideTests. Now I would like to examine
the
difference in which probesets are called by the various methods.
I've...read everything I can find about the venn tools in limma and
vennSelect, but they only seem to compare the output of different
contrasts
within a single dataset. Can someone
by Feature Extraction software; this software provides some
flags measurements in the file.
In limma manual the authors showed an example with Agilent single
color arrays: Time Course E ects of Corn Oil on Rat Thymus with...in this they filtered out control probes
and low expressed probes.
I couldn't find in the manual if limma takes the flag measurement
parameters to process data. If not, does…
<div class="preformatted">
I have been using B values to rank genes in order of more likely to
less likely (differentially expressed) in LimmaGUI.
I am now using Limma, I noticed the default value for the parameter
"proportion" (on the function eBayes) is set at 0.01 (expected 1%
differentially expressed genes). I didn't pay much attention to this
parameter before, because in LimmaGUI you …
<div class="preformatted">Dear Ingrid,
You are getting yourself into knots here. It is
easier than that. The following should work fine
x <- lumiR("yourIlluminaSummaryFile")
y <- lumiT(x)
y <- lumiN(y, method="quantile")
fit <- lmFit(y, design)
Note that lumiT() is analogous to vsn but
customised for Illumina data, and it returns
expression values …
updated 18.3 years ago • Gordon Smyth
1) Residual standard error
2) Multiple R-Squared
3) Adjusted R-Squared
4) F-statistic
With limma, and eBayes, I deduce (incorrectly?) that efit$F and
efit$F.p.value
convey information similar to number 4 above. How about
div class="preformatted">Hi all,
I got differentially expressed genes using limma from Agilent single
color
experiments (3 normal and 3 tests). I would like to do a hierarchical
clustering and also generating
updated 17.7 years ago • Abhilash Venu
Hello, I had a question about extracting covariate-corrected normalized count values from limma (if possible) for box plots. Essentially, I have some genes which limma labels as differentially expressed when covariates...Hello, I had a question about extracting covariate-corrected normalized count values from limma (if possible) for box plots. Essentially, I have some genes which limma labels as …
updated 2.6 years ago • phelankj
I've made a couple of trivial modifications to the mroast function in limma to enable parallel processing (otherwise with a high rotation number and a big set of genesets it can take a while to...I've made a couple of trivial modifications to the mroast function in limma to enable parallel processing (otherwise with a high rotation number and a big set of genesets it can take a while to run
updated 10.8 years ago • alexgutteridge
upgraded my mac to high sierra and are in need of rum´nning edgeR- the problem is that the package limma does not work under the R-version that I am forced to use (3.4.3)- so does anyone know if there is a way around this, or if the
gt;>
>> I would very much appreciate your comment on the experiment design
in
>> LIMMA. It is about processing of experiments with multiple
>> treatments.
>>
>> Let's say we have a simple Affy experiment...together (normalise them together and fit linear fit models
>> using the whole dataset) in LIMMA we wi…
updated 18.6 years ago • James W. MacDonald
Hi all,
I wanted to know if it is possible to remove 3 batches using "limma".
I have sequencing data with three possible batch effects: age, gender and working sets.
As far as I understand, using limma
updated 5.9 years ago • Matan G.
organs are obtained from the same mice. I would like to model the effects of individual mice using limma's random effects via `` duplicateCorrelation ``. As library sizes are very consistent across all samples (and I might want...to play around with `` genas ``), I was thinking of using limma-trend.
I've seen some posts on using `` voom `` and `` voomWithArrayWeights `` together with `` duplicat…
updated 8.3 years ago • maltethodberg
analyzing 24 affy slides taken from GEO, 12 slides for each of
the two
conditions. According to the limma vignetetts chapter 8.5, I can have
kinds
of two design matrix. What are the differences?
So I can either do "treatment-contrasts
<div class="preformatted">Hi limma users,
I have a questions about the MA-plots.
I try to save a number of graphs to one pdf-file which works for
image-plots and...div class="preformatted">Hi limma users,
I have a questions about the MA-plots.
I try to save a number of graphs to one pdf-file which works for
image-plots
12:08 -0500
> From: Wei Xu <xuwei3 at="" msu.edu="">
> Subject: [BioC] reference argument in limma factorial design
> To: bioconductor at stat.math.ethz.ch
> Content-Type: text/plain
>
> Hi, everyone,
>
> I am working...is what the coefficients now mean. Please refer to the
examples
on common reference designs in the limma User's Guid…
updated 17.0 years ago • Gordon Smyth
<div class="preformatted">
Dear list,
I have a doubt about the real use of spots weights
during
normalization in limma. According with the documentation spots
weights
equal to 0 are ignored during normalization (and other
posterior
analyses...list,
I have a doubt about the real use of spots weights
during
normalization in limma. According w…
updated 19.9 years ago • Ana Conesa
<div class="preformatted">I realize this may be a silly question, but I have gone through all
the
case studies in the limma users manual and I can't seem to find the
answer to this anywhere. I have a 3x3 factorial experiment and I
followed the case...I realize this may be a silly question, but I have gone through all
the
case studies in the limma users manual and I can't seem to find the
…
updated 19.6 years ago • Ivan Baxter
div class="preformatted">Hi,
I am using limma to analyse a 2-colour microarray experiment. There
are 2 treatments and 4 replicates in each of these groups. Each
replicate
updated 21.7 years ago • Danielle Fletcher
div class="preformatted">Hi people,
I execute this step in limma and I have a error below:
> RegianeSample <-
read.table("regianeRicoPobre.txt",header=TRUE,sep="\t",as.is=TRUE)
> RegianeSample...1, 2 or 3;
Please, any tip are welcome and/or one step by step to analyze imagene
out
put file in limma is very apreciate!
Thanks
Marcelo
---</div
I want to use BMI as a continuous outcome variable. Not to divide in groups.
To do this, I use limma. But I am not sure limma is suitable to directly use continuous variable as outcome based on no divide groups.
If i cann...I want to use BMI as a continuous outcome variable. Not to divide in groups.
To do this, I use limma. But I am not sure limma is suitable to directly use continuous varia…
for generating plots that demonstrate the differential expression
statistics calculated from voom/limma. What do you recommend? FPKM
plots don't always agree with my voom/limma results.
For example, if the differential expression...results from limma report
a log Fold change of 2 for group A vs. group B, I want a plot (e.g.
boxplot, bar graph, etc.) which visualizes this difference...that you
pr…
updated 11.9 years ago • Heather Estrella
Hello,
Apologies in advance if this post is too general for this forum.
I'm aware that the limma framework can be used for differential expression analysis at the pathway level with GSVA:
https://www.bioconductor.org...Hello,
Apologies in advance if this post is too general for this forum.
I'm aware that the limma framework can be used for differential expression analysis at the path…
div class="preformatted">Dear Birger,
Don't forget to state your limma version when you ask a question.
Almost certainly you have a
slightly out of data version. Reinstall limma and the example...Hauchecorne Birger" <birger.hauchecorne at="" student.ua.ac.be="">
> Subject: [BioC] marray and limma error with lmFit
> To: <bioconductor at="" stat.math.ethz.ch="">
&am…
updated 18.7 years ago • Gordon Smyth
I used RUVseq to get the factors of unwanted variation and ran these data through voom and limma using the following code:
_require(RUVSeq)
require(EDASeq)
require(edgeR)
require(limma)
require(dplyr)_
_\#Input data matrix...nbsp; design=limma.design\_matrix, plot = FALSE, save.plot = FALSE)_
_\#Use limma to perform DE analysis for each norma…
<div class="preformatted">Dear list,
here a question about the appropriate design of a specific test layout
for use with limma. The problem seems almost trivial, but among the
numerous postings I haven?t found something resolving my problem :
I have...Dear list,
here a question about the appropriate design of a specific test layout
for use with limma. The problem seems almost trivial, but …
class="preformatted">Dear Prasad,
You don't need to worry about setting up the contrast matrix, as limma
will do this for you. You can use makeContrasts() and tell it
directly
what comparisons you want to do. For example:
cont.matrix...get the idea. You can ask for any number of comparisons. There
are
many examples of this in the limma User's Guide.
With respect to your first questio…
<div class="preformatted">Dear Jose,
My suggestion: don't remove the empty spots in the first place.
Best wishes
Gordon
> Date: Mon, 2 Mar 2009 09:48:48 -0600
> From: Jose Coria <com90185 at="" gmail.com="">
> Subject: [BioC] limma printer layout
> To: bioconductor at stat.math.ethz.ch
>
> I'm trying to plot background intensity after clean…
<div class="preformatted">Dear limma experts,
I am analyzing the data set given to me and described by these the
column names of my MA object:
> colnames(MA.hyp)
[1] "../ampcon/mev/C0-_1stround_vs_C60-_1stround_13263536.mev"
[2] "../ampcon/mev/C0-_2ndround_vs_C60-_2ndround_13263534.mev"
[3] "../ampcon/mev/C60-_1stround_vs_C0-_1stround_13263533.mev"
[4] "../ampcon/mev/C60-_2ndround_…
on these or related methods. But have you
read
Section 10.3 "Testing across contrasts" in the limma User's Guide
which
discusses these methods? You might also find it helpful though to
search
for my replies to previous...gt; From: Michal Kol?? <kolarmi at="" img.cas.cz="">
> Subject: [BioC] Methods in decideTests (limma)
> To: bioconductor at stat.math.ethz.ch
> Messa…
div class="preformatted">Dear all.
I have used Limma to analyse my data and I got no differentially
expressed genes correcting with multiple testing using fdr. Then a
colleague...and got
~600 genes with an fdr < 0.05.
I immediately thought I had done something wrong in my Limma analysis
and double checked a zillion times but I couldn't find any errors.
When I compared the ranking for …
use it is easier in Imagene
to do
it the way as I wrote before. Maybe for a inbetween solution limma
could
automatically cut the file into multiple separate arrays (1.a 1.b
1.ect) . I
think for normalization (printip and...might have to read in your data manually using
read.table()
or similar.
>> Secondly, using limma and the targets <- readTargets function you
>&…
updated 21.1 years ago • Breuk102
to be working to me!
Regards
Gordon
----- original message ------
[BioC] Undesirable behavior of limma MArrayLM?
Paul Leo p.leo at uq.edu.au
Thu Jun 26 09:33:59 CEST 2008
Personally I don't like this kind of behavior see "#*** and...gt; fit2$genes[n,"ID"]
[1] "106220736"
> class(fit2)
[1] "MArrayLM"
attr(,"package")
[1] "limma"
> sessionInfo()
R version 2.7.1 RC (2008-06-16 r45…
expressed genes (Code below). I approached this as a 5x2 factorial
problem and took my lead from the limma guide (ch 8.7). ?When calling
topTable for any contrast, the list of P.Values contains a range of
values (small small, some...Any idea why my q-values are all the same?
################################################
library(limma)
library(affy)
#read in our data
target ?<- readTarg…
Monday, May 20, 2013 7:29 PM
To: Ingrid Dahlman [guest]
Cc: Bioconductor mailing list
Subject: [BioC] Limma, model with several factors
Dear Ingrid,
If you block on subject (as in Section 8.4 of the User's Guide), then
you have automatically...gt; To: bioconductor at r-project.org, ingrid.dahlman at ki.se
> Subject: [BioC] Limma, model with several factors
>
>
> I ha…
<div class="preformatted">Hi Gustavo,
The limma package is actually capable of reading and preprocessing
Illumina data itself. There is an example of this in the Limma user's
guide, which you can access by typing limmaUsersGuide() in R. The
function to read Illumina output is called read.ilmn. Personally I
would take this route rather than going through Partek, as limma also
has other prep…
updated 14.8 years ago • Mark Dunning
div class="preformatted">Dear Lists,
I'm currently using LIMMA package to analyze my microarray datasets.
For each treatment, I have three biological replicates. The subset of
the
updated 13.8 years ago • yeeling chong
Recent ...
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