<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…
Order by: Relevance
div class="preformatted">Dear madam, sir,
I am using Limma with the latest version of bioconductor.
After succesfull loading of my Imagene files I want to load a file
called
SpotTypes.txt...as outlined in the Limma usermanual on page 6.
Reading the spottypes goes well, but when I apply the spotStatus
function I
get the following error...something I do
wrong
or if something is broken in the p…
div class="preformatted">Dear Venu,
limma requires replicates. Pretty much any statistical testing method
requires replicates.
You can run lmFit() without replicates...been given to many posts asking this question over
the years.
I am a bit puzzled what you expect limma to do for you in the absence
of
replication.
Best wishes
Gordon
> Date: Fri, 12 Oct 2012 10:06:40 +0100
>…
<div class="preformatted">Hi,
Im new to limma, and I'm trying to determine a design matrix for the
following type of experiment. I dont see an example of this sort of
experiment which is becoming increasingly common. I have Diseased vs
control (two color). I have 30 diseased individuals, and each
individual has had 4-6 technical replicates carried out with dye swaps
involved. My question is…
div class="preformatted">Dear Michael,
Thanks for your comments on limma and for your email. I definitely
agree
with you that constructing the design and contrasts matrices are the
hardest...part of using limma - the amount of time I spend advising
people on
this makes me very aware of it. You're not the only person to have
asked
about...is a direct design
while
you have a common reference de…
preformatted">Hi
I just wondered if anyone knew how to use the plotPrintTipLoess()
function in limma with the R function split.screen()? When I try,
plotPrintTipLoess() uses the whole window, rather than just drawing in
the
div class="preformatted">Dear Gordon and limma users,
I'm struggling to understand the design matrices in
the Weaver Data in the Case Studies section of the
limma User
stages of the disease. I've earlier used rowttests and FDR
correction. Now I was playing around with limma to see what I could do
(added different covariates etc) but also investigated the most simple
setting, comparing the...different stages directly using Limma. The
first thing that struck me was that limma "finds" only half the amount
of significantly diff expressed genes. So I started...to lo…
updated 17.5 years ago • Boel Brynedal
preformatted">We would like to adjust our ANOVA-type analysis by using the
covariate "age". Because limma is based on contrast, rather than
"type III SS", it seems to me that the only way to proceed with an
ANCOVA-type analysis is
div class="preformatted">This isn't an error in limma of course, rather you have tried to use a
function (write.table) on an inappropriate object. Do you want to
output
the normalized...your_file.txt",sep="\t")
Gordon
At 03:00 AM 1/12/2003, utepandragon@tiscali.it wrote:
>I use Limma Dev. Package and i'd like output my normalized data, but
i
>have a problem:
>
> &…
<div class="preformatted">Edmund Chang wrote:
> Hi Jim,
> Thank you very much for the many tips! I really do appreciate it. I
do
> have another question about p-values associated with F-statistics.
> results<- decideTests(fit.all, method="nestedF", adj="none"
>
> In the limma user guide, it says the following about F-statistic
(Sec 18):
&…
updated 19.9 years ago • James W. MacDonald
From: Naomi Altman <naomi at="" stat.psu.edu="">
> Subject: [BioC] problem read.maimage("Agilent") -limma
> To: bioconductor at stat.math.ethz.ch
>
> I am having trouble reading the Agilent arabidopsis 22575 gene array...using
> read.maimage in Limma under R 2.1.1 (I don't know the limma version,
but I
> just downloaded using the R packages interfac…
updated 20.5 years ago • Gordon Smyth
<div class="preformatted">Hi all,
I was wondering if I could get some constructive feedback on some code
I'm using to analyze an Affymetrix repeated measures experiment. I've
found through the list that limma's repeated measures capabilities are
limited when it comes to specifying certain correlation structures,
but I really like the way it handles contrasts, so I tried to find a
way to f…
based on the expression profile of all
the genes as a whole. I have a situation where I perform limma with
eBayes and have repeated it using t.test and the multtest library (so
without variance estimation) and have found...that the p.values from
limma
are larger than those found using the traditional approach.
Arising from this I have a few questions:
1) When should use...there anything wrong w…
div class="preformatted">Hi all,
I am using limma on Affymetrix data and want to fit a linear model
with
fit <- lm.series(exprs(E), design)
My question is:
Is the data in E supposed
div class="preformatted">Hello:
I am a new user for limma and trying very hard to understand how to
use it.
Could I ask why is the statistical different between the normal "lm"
and
<div class="preformatted">> Date: Tue, 19 Jul 2005 10:53:37 +0200
> From: ?pela Baebler <spela.baebler at="" nib.si="">
> Subject: [BioC] Gene filtering for differential expression (limma)
> To: <bioconductor at="" stat.math.ethz.ch="">
>
> Hello everyone!
>
> We are struggling to implement R for the analysis of two color c…
updated 20.5 years ago • Gordon Smyth
div class="preformatted">
I have carefully read the Limma users guide but still have not sorted
out how I design the contrasts for the following Project.
In want to compare the...like
a batch effect.
Is it possible to block for two factors, suject and center, in the
same test in Limma?
/Ingrid
-- output of sessionInfo():
See section 8.7 in the user guide.
--
Sent via the guest posting fa…
A values (if you calculate manually). Somehow, between
loading
>and calculation of the A values, limma is adjusting these buffer
values so
>that they are spread across the range. I have checked everything I
can
>(i.e. are...matrix. They are.
>
>As a final check, I plotted the same data in Genetraffic, and then in
>limma (both non-normalized), with the buf…
updated 22.0 years ago • Gordon Smyth
<div class="preformatted">Dear Christian,
See Section 8.2 of the limma User's Guide. The 'block' argument of
duplicateCorrelation() and lmFit() handles random effects.
Best wishes
Gordon
> Date: Fri, 25 Sep 2009 08:33:43 +0200
> From: Christian Bri?re <briere at="" scsv.ups-tlse.fr="">
> Subject: [BioC] mixed models analysis with limma
> To: bioconducto…
updated 16.3 years ago • Gordon Smyth
div class="preformatted">Hi,
I would like to use limma to analyse affymetrix data, but my affy
data is not an eset object because I have done the low-level analysis
in a different
as afterwards one would add the peptide count and then run `spectraCounteBayes` to adjust. Or since `limma` ~3.52, run a DEqMS like analysis directly by using the peptide/features count as `TREND = Peptide.Count` on `eBayes()`.
The `limpa...vignette example uses the default, `eBayes(fit)`. On the `limpa` manuscript it is written that all `limma` analysis included the trend verison. *...limma-t…
<div class="preformatted">Hello everyone!
We are dealing with a quite straightforward microarray experimental
design on TIGR potato cDNA microarray. We
Here is a brief description of the experiments: we hybridise virus-
infected versus mock-infected potato plant RNA from several potato
cultivars - each microarray is hybridised with RNA of the same
cultivar - but there is no common referen…
updated 20.5 years ago • Matjaž Hren
all,
I am analysing data of a methylation experiment using golden gate
Illumina assay. I use the LIMMA package. Illumina?s beadstudio was
used to obtain the normalised data which is a continuous variable
(range 0-1). The analysis...the log scale is not essential. However I am not completely sure. My
question therefore:
Can the LIMMA package also be used for data that is NOT on a log
scale?
Man…
correction. I am no its not
recommended,
but its the situation I have to deal with.
How do I use limma without eBayes? I read somewhere that it is in the
Limma's user guide but I can't for the life of me find it.
Thanks
Dan
--
**************************************************************
Daniel
Hi, I am using Agilent single channel data and found the `limma::avereps` function handy, since the number of replicate probes on the array vary per gene (locus). However, I would prefer...function to get the **median** in stead of **average**? Or is there another function available in `limma`? I mean I can of course try `dplyr` or some similar package to calculate median per group (probe set), b…
updated 6.1 years ago • b.nota
Hi all,
When I run limma compare disease vs control, the design object has two columns. However, when I adjust for covariates: sex (factor with...Hi all,
When I run limma compare disease vs control, the design object has two columns. However, when I adjust for covariates: sex (factor with 2...design)
Error in eval(ej, envir = levelsenv) : object 'group_vectorCN' not found
Is that limm…
updated 18 months ago • Chris
got the result below.![enter image description here][1]
I then corrected the batch effect with Limma and was able to get a better PCA result:
![enter image description here][2]
Do I use the Limma batch corrected values to perform
updated 22 months ago • sap275
div class="preformatted">Hi
I've been using the limma and eBayes function for looking at a set of
affymetrix chips with 8 or so different groups within. Following the
instructions
<div class="preformatted">Gordon wrote:
>This isn't an error in limma of course, rather you have tried to use
a
>function (write.table) on an inappropriate object. Do you want to
output
>the...div class="preformatted">Gordon wrote:
>This isn't an error in limma of course, rather you have tried to use
a
>function (write.table) on an inappropriate obje…
data
from the results of an eBayes result from a continuous variable linear
model run with limma. I have thus far not been able to locate
documentation on how to achieve this, and any assistance would be
greatly appreciated
When I tried to update, I receive an error..
Any advice, How do we solve this issue?
> biocLite("limma")
BioC\_mirror: https://bioconductor.org
Using Bioconductor 3.4 (BiocInstaller 1.24.0), R 3.3.2 (2016-10-31).
Installing package...to update, I receive an error..
Any advice, How do we solve this issue?
> biocLite("limma")
BioC\_mirror: https…
updated 8.7 years ago • bioadept
0100
> From: "Endre Sebestyen" <endre.sebestyen at="" gmail.com="">
> Subject: [BioC] basic limma questions
> To: Bioconductor <bioconductor at="" stat.math.ethz.ch="">
>
> Again :
>
> Hi!
>
> I'm a beginner in limma and...d like to ask a few
> basic questions.
>
> I wrote the following script :
&g…
<div class="preformatted">
>Date: Wed, 30 Nov 2005 04:13:03 -0800 (PST)
>From: bregje wertheim <bregjewertheim at="" yahoo.com="">
>Subject: [BioC] normexp (limma) failure?
>To: bioconductor at stat.math.ethz.ch
>
> Dear all,
>
>since upgrading to the latest version of R (2.2.0) and the latest
version
>of limma (2.4.4), …
Hello,
I am new to the field and wonder what the differences are between edgeR and limma as both are recommended for RNA-seq and other applications.
Tried reading the papers and manuals but my stats background...same data with two different models, either a linear or a negative binomial one?
- Why exactly is limma so much faster, does this has to do with the models`?
- Does limma estimate a disp…
updated 3.8 years ago • jose.carmeliet
<div class="preformatted">Dear List,
I have a question concerning missing values in limma. Consider the
following short example:
M = rbind(c(10,9,5,4,5,12,13,7,8),c(10,9,5,4,5,12,13,7,8))
w = rbind(c(1,1,1,1,1,1,1,1,1),c(1,1,1,1,1,0,0,0,0))
class = factor...div class="preformatted">Dear List,
I have a question concerning missing values in limma. Consider the
following short example:
…
div class="preformatted">Hi all,
I recently used the linear model fit in limma to rank differentially
expressed genes between treated vs. control with a data set. The data
includes three log2(Treated...below background,
saturated, low intensity, or non-uniform. I am wondering how the
linear
model in limma handles missing values and why a gene with only one
data
point is identified as a high …
<div class="preformatted">Hi,
We are just beginning to use the limma software, specifically with the
GUI interface and are running into some problems. Our array has
duplicate spots in a...div class="preformatted">Hi,
We are just beginning to use the limma software, specifically with the
GUI interface and are running into some problems. Our array has
duplicate spots in...top to bottom m…
Hi,
I have a 3 questions that are somewhat related:
I noticed a discrepancy between the Limma vignette (21 Nov 2005) and
readTargets() in Limma 2.4.4 (complete sessionInfo at the end). In the
vignette on pg. 12, it says you...so why it
doesn't
work for assignment?
This may or may not have something to do with the version of Limma...
which
leads me to my last question: Why does the development …
div class="preformatted">Dear Listers,
I have a working Limma script below, but I don't know what the output
is comparing. Can anyone give me a clue? Also, you can see from my run
that i am...lt;-
c('1st_litter','WT','2nd_litter','WT','1st_litter','2nd_litter','WT','
1st_litter')
require(limma)
design <- model.matrix(~ factor(sampleType))
colnames(design) <- c('1st_litter', '2nd_…
so R(2.8), Mysql(v?) and the
databases are installed remotely and I use them through bash with ssh.
*Limma*
I did an RMA on my data following the tutorial. I have 4 biological
replicates in 2 groups. I would like to run LIMMA on my...parent.mathieu@gmail.com
McGill University
Nosciences and Neurosurgery /// Center for Bioinformatics
Limma Script
*pairwise <- function(rma.data,group,gp1,…
div class="preformatted">Hi,
I am using Limma for a non-affy single channel dataset. the design is
a 2X2
factorial design, but one chip is missing.
array gender genotype
<div class="preformatted">Estimated colleagues,
It is probably a simple question, but I am new to limma and I don't
find
the answer.
I have a matrix with columns corresponding to different experiments or
samples, and rows corresponding...div class="preformatted">Estimated colleagues,
It is probably a simple question, but I am new to limma and I don't
find
the answer.
I have a matrix …
div class="preformatted">
Hello everyone,
When I try to load my illumina bead summary data into limma i get the
following error msg:
library(limma)
x <- read.ilmn(files="ProbeProfile.txt",
ctrlfiles="ControlProbeProfile.txt
div class="preformatted">Hello,
I have installed limma GUI and I'm trying to repeat
some analysis that I did before with limma.
When I try to Normalize Within arrays using the
yan <01.weili@gmail.com>
To: <bioconductor@stat.math.ethz.ch>
Subject: [BioC] how to get the LIMMA required files for analysis from
Illumina Methylation450K chip assay
Message-ID:
<caeqrnaftel-o1+qa7ozoxol+2esc_qfzggj...Illumia GenomeStudio-Methylation software.
My question is how can I extract data files required by LIMMA?
I hope to genotype the differential …
01/03/2006 9:59 PM
To: michael watson (IAH-C)
Cc: bioconductor at stat.math.ethz.ch
Subject: [BioC] Limma and time-course data
Dear Mike,
limma does exactly what you want. The approach outlined in the User's
Guide (and in the workshop...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
co…
<div class="preformatted">Hell everyone!
I am trying to do single-channel normalization for my serverl slides
using limma. After I read the userguide of limma, I made a Targets
file.It is just like:
SlideNumber FileName Cy3 Cy5
1 2004-4-2-cy3(450)-0409-Con-only532.gpr Con Blank
2 2004-4-2-cy3(450)-0410-A24h-only532.gpr A1h Blank
3 2004-4-2-cy3(450)…
updated 21.6 years ago • xpzhang
preformatted">
>Date: Sat, 21 Jun 2003 00:37:37 EDT
>From: Phguardiol@aol.com
>Subject: limma and affy
>
>Sir,
>I m trying to use limma after having extract background and normalize
my data
>(HU133A chips from...gt;between these 3 groups.
>here is what I tried to do so:
>library(affy)
>library(limma)
>data <- R…
div class="preformatted">Dear All,
I have a question about limma model.
We have 5 subjects, each subject has 9 time points data, so I want to
find
DE gene. Based on limma manual, it reported
I have the following limma code which I wrote(dummy)
The matrix is designed in a way so that I don't use the intercept part.
library(limma)
d <- matrix
<div class="preformatted">
>Date: Tue, 11 Apr 2006 15:08:55 +0000
>From: Adaikalavan Ramasamy <ramasamy at="" cancer.org.uk="">
>Subject: [BioC] LIMMA: testing for batch effects
>To: BioConductor mailing list <bioconductor at="" stat.math.ethz.ch="">
>
>Dear all,
>
>We have 63 arrays that are either diseased or normal. We w…
cel files through RMA log 2 transformation (code is given below) i want to do linear models limma so for that i follow linear model limma tutorial (the code is given below) there is an error kindly if some one know about...linear models"limma" so guide me. I read in another tutorial about target files but i dont understand the criteria of selecting target files...1,1,2,2,3,3,3)))
&…
updated 8.8 years ago • nia
I am analyzing my first 2-color array experiment (Agilent arrays).
After
reading the manual of LIMMA and the book BioC case studies, I decided
to
use LIMMA applying VSN normalization. However, to me it is not
completely clear...which arguments are passed to VSN when executed from
LIMMA.
>From ?normalizeBetweenArrays i learn:
"method="vsn" uses the vsn function from the vsn package. For th…
updated 16.3 years ago • Guido Hooiveld
07 Feb 2006 10:34:15 -0500
> From: Jianping Jin <jjin at="" email.unc.edu="">
> Subject: [BioC] limma anova table?
> To: BioConductor_list <bioconductor at="" stat.math.ethz.ch="">
> Message-ID: <c8b2be8836479e5ed6585fdf...gt; Content-Type: text/plain; charset=us-ascii; format=flowed
>
> Dear limma developer and list:
>
> I am…
<div class="preformatted">
>Date: Tue, 12 Jul 2005 12:53:32 -0700
>From: "Wu, Xiwei" <xwu at="" coh.org="">
>Subject: [BioC] Limma: A values in topTable
>To: bioconductor at stat.math.ethz.ch
>
>Dear list,
>
>I did a search in the mail achive, and did not find anyone reporting
the
>same issue below.
>I was looking a…
Dear all,
I have a question on a subject that I think was not discussed here
before.
I am using limma package for the detection of significant differential
expression in an affy experiment:
3 "Healthy" (group1) indiv. before...i.e.
group4-group1,
group5-group2, etc). I used these commands:
>library(affy)
>library(limma)
>library("hgu133a")
>x<-ReadAffy()
…
to
get specific information from them. We have only seen two BlueFuse
files, and can only base our
limma support for the BlueFuse platform on what we've seen.
We could supply robust support from BlueFuse files in limma if we...From: "Eskeatnaf, M.A." <eskeatnaf.ma at="" vumc.nl="">
> Subject: [BioC] bluefuse export and limma read.maimages
> To: <bioconductor at="" stat.m…
div class="preformatted">Hi folks, I'm analyzing microRNA data using limma and I'm wondering
about
the validity of the p-values I'm getting out. Its a simple 'Group A Vs
Group
B' experimental design...t-test you get p=0.008, which then also needs to take
the
multiple test hit. Can anybody explain why limma is giving me such
lower
values and if they are valid?
I can provide more information if…
div class="preformatted">
Hello all,
I have a question while I am using the limma package to
identify
differentially expressed genes: should I perform gene filtering
after
normalization to exclude...no
noticeable
effect on the final P-value and therefore had not been required, so
I wonder
if limma's capability to detect differentially expressed genes
would be
affect…
updated 16.2 years ago • Peng, Fred
Recent ...
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