<div class="preformatted">hi,
i am doing analysis for 10 breast cancer arrays (two color Agilent4x44
arrays) with limma,where Cy3 is normal and Cy5 is tumor.And all are
biological replicates ,means all 10 arrays have been prepared from 10...hi,
i am doing analysis for 10 breast cancer arrays (two color Agilent4x44
arrays) with limma,where Cy3 is normal and Cy5 is tumor.And all are
biologi…
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<div class="preformatted">Hi Gordon,
I've been out for a while and finally read your detailed reply.
Thanks so much - it really helps clarify things for me!!
Cheers,
Jenny
At 05:55 PM 11/27/2008, Gordon K Smyth wrote:
>Hi Jenny,
>
>Should blocks be fixed (in the design matrix) or treated as random
>(hence enter the covariance matrix as correlations)? This que…
![enter image description here][1]
Hello everyone,
I'm trying to analyse microarray data from Affymetrix. I am analysing a study in GEO database with a number:GSE49893. Unfortunately I have stumbled upon a problem. When using a 'alias2SymbolUsingNCBI' function the output is showing that GeneID, Symbol and type_of_gene is 'NA'. When I checked the eset data by going into featureDATA and then …
updated 3.6 years ago • Prometheus405
<div class="preformatted">Hi Qin,
On Thu, May 13, 2010 at 11:38 AM, qin kuang <kuang_qin at="" hotmail.com="">
wrote:
> Thanks Steve.
>
> Actually I have done this family by family. I also tried method like
GEE to
> take familial relationship by averaging technical replicates. At
this point,
> looks the methods like LIMMA/GEE can not? two-level/type…
Dear Al,
No research papers (to my knowledge) have been written yet on multiple
testing for the hierarchical linear model, so I can't refer you to any
literature.
Use "separate" if you want to get the same results as topTable(). The
great advantage of this method is that you'll get the equivalent
results
regardless of which set of contrasts you test together. This is fine
for
each contrast bu…
<div class="preformatted">Hello,
I found that the question was already answered, but the solution
proposed did not work for me.
Could you please help to resolve an issue with limma I faced. Please
see the attachment. I have a set of arrays for 4 groups of patients
(Atype) taken at two time points (Visit). Every...but the solution
proposed did not work for me.
Could you please help to res…
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 Gordon,
I just downloaded the new R 2.8.0 release and limma 2.16.0. I was
checking out the new sort="none" option in topTable and I found an
error in the help page for ?topTable. It doesn
<div class="preformatted">Hello,
I'm using limma to analyze affymetrix arrays from a time course
experiment (time points 0, 2, 7, 24). We are interested in comparing 0
vs 2, 0...div class="preformatted">Hello,
I'm using limma to analyze affymetrix arrays from a time course
experiment (time points 0, 2, 7, 24). We are interested in comparing 0
vs 2
Jun 2009 13:53:19 +0000
> From: Juana Arco <luana_arch at="" hotmail.com="">
> Subject: [BioC] Limma - GenePix
> To: <bioconductor at="" stat.math.ethz.ch="">
> Message-ID: <snt109-w62ce4e25ce69389a9bf63eff360 at="" phx.gbl
updated 16.5 years ago • Gordon Smyth
div class="preformatted">Hi folks,
I am fairly new to limma. I hope that someone could help me out with a
design metrix and contrast. Factors are: 1st - drug response
(responder
versus
time course analysis with Bioconductor package maSigPro? Similar to how covariates can be used in limma model
updated 8.3 years ago • veersingh.marwah
Hello,
I am trying to use limma to analyze data from a microarray experiment.
This is what I got from the contrasts I am interested in.
<pre>
> summary...Hello,
I am trying to use limma to analyze data from a microarray experiment.
This is what I got from the contrasts I am interested in.
<pre>
> summary(results
updated 10.7 years ago • Bandyopadhyay, Somnath Som
div class="preformatted">Did something change between versions of Limma for R 1.8.1 and 1.9.0
that I
missed? Where did the NAs come from? These are the results from
running
topTable on four dye...topGenes <- topTable(eb,number=30,
adjust.method="fdr",genelist=genenb,
sort.by="B")
R 1.8.1 and Limma 1.3.11
AA936757 3.719032040892476 13.29244868974321
21.273219140535428 1.77…
from `` RSEM ``. My understanding is that I can pass the expected counts to `` voom `` and then `` limma `` even though raw counts is more ideal. I just wanted to check that this is correct?
Thanks
Hi,
I am using limma to analyze a barcode sequencing dataset. The raw data are counts, similar to RNA-seq. I am using `` edgeR::calcNormFactors...I have looked around and found `` plotCounts `` function from DESeq2. Is there a similar function in limma? If not, is there another package that provides such a function for EList or ExpressionSet objects?
Thanks.
Yury
 
updated 9.6 years ago • Yury Bukhman
<div class="preformatted">Lots of posts today....
Actually this may also be of interest to others with similar designs.
I remember reading on a previous thread that even with low (<3 reps)
you
could still use a linear model to estimate significant changes. Rather
than just ask if this is really possible I decided to do it myself
before seeing what others have to say. I know limma s…
soon.
Another thing on my "TO DO" list for limmaGUI is to make the GAL
file optional like it is in limma. It makes sense to require a
GAL file for "Spot" image analysis files which is what I started
out using, but it shouldn't be
updated 21.5 years ago • James Wettenhall
div class="preformatted">
Hello !
I try to use LIMMA according to common reference design as descripted
in
the User's guide.
The data are stored in variable RGraw:
>QAfile
Hi,
I am trying to build a model matrix in limma to perform differential analysis of my features. I have a simple phenodata like this:
Sample condition
dmso_1 control
p/68196/\#68309), i would like to ask you about the important issue of annotation of illumina in limma. As i have preprocessed and analyzed the data with limma, i searched ways to convert the probeIDs to nuIDs in order to have
updated 10.6 years ago • svlachavas
line. The matrix is the log expression ratio(12hrs_con/0hrs)and (12hrs_trated/0hrs).
Can I use limma to get the DEGs using the my matrix as direct input file?
#I have 2 replicates (each with control and treatment). I designed...0.1220447
6 4931406P16Rik -0.00345034 0.06384793 -0.07985070 -0.1200976
Is it okay to use limma on my matrix data ? is the design is correct?
Thanks
updated 7.0 years ago • shuvadeep.maity
div class="preformatted">I have been using limma to do differential analysis between two
different groupings, both splitting the samples into two groups. The
results
<div class="preformatted">Dear Jose,
The warning from lmFit was introduced a while ago (a year or so) as a
result of a user request on this mailing list.
The warning is to remind people that, when some of the coefs for a
particular probe become NA but others are estimable, the
interpretation of
the remaining coefs is changed for that probe. This is an unavoidable
characteristic of missin…
Hi,
I was wondering is there a way to include baseline gene expression as covariate in model matrix formula for limma?
I have microarray data from clinical trial patients in a control and an intervention group and I want to adjust for baseline...is there a way to include baseline gene expression as covariate in model matrix formula for limma?
I have microarray data from clinical trial patien…
updated 4.0 years ago • S
<div class="preformatted">Hi,
thank you, that solved most my problems. But of course this is where
new
problems arise.
Anyhow, this aspect works nicely, thanks for pointing me at the right
direction.
Best regards
Maxim
2010/3/31 James MacDonald <jmacdon@med.umich.edu>
>
>
> Maxim wrote:
>
>> Hi,
>>
>> I have a q…
updated 15.8 years ago • Maxim
In limma paper in 2015 (https://academic.oup.com/nar/article/43/7/e47/2414268), it stated that it accommodates unequal variances...section titled "Variance models allow for unequal variability". My question is that should we assume Limma deals with unequal variability automatically or should we set some parameter(s) based on estimation using our data
Hello,
I just started working with limma and so far followed the limma users-guide to recive a TestResults Object.
I've printed the results into a file using write.fit...make sense to treat as significant annotated genes differently?
I just started to deal with limma and (microarray data in general) during my current semester, so please go easy on me in case I missed something obvious
updated 9.3 years ago • bi_Scholar
11 rows
> each mir has 4 replicates
>
>For analysis of the data I use limma GUI, to obtain the p-values of
>differentially expressed mirs I carried out loess normalization
>(backgroundsubstraction...distance, using the number of spots of
row
>distance results in dims[product 0]).
>I read the limma guide and checked also the examp…
div class="preformatted">I just used intraspotCorrelation as suggested in the online Limma
documentation for single channel analysis.
Over half of my estimated correlation coefficients are bigger than
1.0
updated 20.2 years ago • Naomi Altman
I've performed a limma differential expression analysis of microarray data, and ended having many genes with a p-value lower than 0.05 whose
updated 10.3 years ago • arfranco
Hi there,
I want to do a simple ebayes analysis to find differentially expressed proteins using limma. I have a datset with 2000+ rows with proteins and 20 columns of which 9 are contols and 11 are cases. How should I use the...Hi there,
I want to do a simple ebayes analysis to find differentially expressed proteins using limma. I have a datset with 2000+ rows with proteins and 20 columns of …
div class="preformatted">Hi,
I am using limma for the first time and have a dataset that has some
negative values once the background has been subtracted from the
of between-array weight values, which one
> can get using the arrayWeights() function in the limma package
> <http: 1471-2105="" 261="" 7="" abstract="" www.biomedcentral.com="">? For
> instance, if one array has the weight value - let
it reasonable to do this analysis to extract effects of
b(Genetic),b(Ageing),b(FOXO),b(4EBP) using limma and how to write
matrix in code?
thanks
Zhi Zhang, Ph. D.
Sanford-Burnham Medical Research Institute
10901 North Torrey
Sep 2005 11:50:58 +0200
>From: Dave Berger <dberger at="" postino.up.ac.za="">
>Subject: [BioC] limma layout query (genepix GAL file)
>To: bioconductor at stat.math.ethz.ch
>Message-ID: <433D0A82.B293F5F at postino.up.ac.za...gt;
>Content-Type: text/plain; charset=us-ascii
>
>Hi
>using R version 2.1.1
>limma version 1.9.6…
Hi,
I have been trying very hard to figure out what is going on, and I feel like I've read everything I could get my hands on, but I must be missing something. Any help would be much appreciated.
I did an RNA-seq experiment with 6 groups, and I am making pairwise comparisons between them and find up and down regulated genes. Originally I used DEseq2, but decided to use edgeR and limma as well f…
placebo_20 placebo_22"
- "celltype2_20 celltype2_22"
I am using 8.3 Paired Samples of the limma user guide as my guide for
the
limma design setup.
library("limma")
# Give levels. Will be the names (the unique names of the
bio.replicates...for 47323 probe(s)
Can anyone tell me what's goes wrong my design?
Or suggest how to do the limma analyses with my
specific experiment.
> sessio…
and did not find anyone reporting
the
same issue below.
I was looking at some cDNA array data using Limma 2.0.2 with
R2.1.1patched under Windows2000. I have three different contrasts.
When
I looked at the topTables generated...gt; library(limma)
> targets <- readTargets()
> targets
SlideNumber
FileName Cy3 Cy5
2005-07-06_04J12 HsKGV_17_(…
At 03:07 PM 10/06/2003, you wrote:
>Dear Dr. Smyth,
>
>I am interested in your R package LIMMA.
>I want to use the function BWSS in this package, but
>I am not sure the meanings of the arguments of this function
>
div class="preformatted">Hi *,
attached is a small patch for limma's read.imagene function, to read
each files' header and not just the first one. Reason: all files may
not have the same header...thus not the same "skip" amount.
yves
-------------- next part --------------
--- limma/R/input.R~ 2003-09-27 08:42:21.000000000 +0200
+++ limma/R/input.R 2003-09-29 17:34:39.000000000 +0200…
updated 22.3 years ago • Yves Bastide
correct the counts for additional analyses (e.g. PCA, clustering), and we were thinking on using limma::removeBatchEffect.
Here comes the question: on which data can we use this function?
Vst, rlog, log2CPM appear adequate...to log2 the counts/TPM before applying the function?
Any advise against using counts treated with limma::removeBatchEffect for subsequent differential expression analysis …
Hi!
I have a question about using the Limma package, lmfit() and ebayes in R which I was hoping someone could answer.
Briefly, I want to use the Limma package and the eBayes
I am aware that limma does not have any built-in facility for **testing random effects**, but **I have an idea for how to do it and would like advice...from someone with a better understanding of the underlying mathematics.
Background: I am using limma to analyse differential expression in a dataset with repeated measures from the same individuals. There are too many
updated 6.4 years ago • c.taylor
div class="preformatted">I just had a question/concern about P value calculations in Limma (I
am
using latest version of Bioconductor)
I recently ran 3 arrays through my analysis. The slides were
analayzed
with
genes between
dissese A and B. There are two type of batch effect in my analysis. I
want to use limma to remove two type of batch effect, one is gender,
another is tissue type. I do as fellow. But I got a error. Is there
some problem
div class="preformatted">Dear list member,
I got an error message when running limma on my array dataset, which
contains a total of four Affy arrays from two different conditions.
Error in if (evar > 0) { : missing
Hi
I have DEG result from limma,now I want to analysis GSEA with "enrichr" service http://amp.pharm.mssm.edu/Enrichr/ ,but it asks me for a weight per
I was asked to run a 2-way ANOVA using LIMMA with strain (AJ, BALBC, C57BL6, DBA, FVB) and treatment (drug, naive, vehicle) as my factors. They want to know which genes change...my reference. The contrasts are different but the F statistics are the same. From reading the limma guide, my understanding is that the factorial 2-way ANOVA needs to have a baseline. Is it possible to…
updated 9.3 years ago • tkhodges
div class="preformatted">WinXP
R 2.0.0
limma 1.8.8
changeLog appears to not accept arguments anymore:
function (n = 20)
{
writeLines(readLines(system.file("doc/changelog.txt...package =
"limma"),
n = 20))
}
Paul</div
updated 21.2 years ago • Paul Boutros
div class="preformatted">Hi,
I tried to read several Imagene files with LIMMA:
library(limma)
targets<-readTargets()
files<-targets[,c("FileNameCy3","FileNameCy5")]
RG<-read.maimages(files,source
updated 18.5 years ago • Yi Xing
model. However when I run the
analysis it
says batch is not estimable.
I am unsure now whether the limma list of differentially expressed
genes is
valid or not, as it might have not accounted for batch variation. (I
do
appreciate
div class="preformatted">
Hi All,
a question about the interpretation of the logFC in limma. I have a
microarray experiment with a common reference (Cy5) design.
I have generated the two matrices in the following
Hello, I am analysing RNAseq data with limma. As input for KNN classification, should I use log2cpm data or voom transformed data? Thank you so much for your consideration
4:55 PM
To: bioconductor at r-project.org
Subject: [BioC] multi-level design and contrasts problem - limma
Hello,
I read the limma user guide on the topics of multi-level experiments
and found the information very useful. But
updated 11.4 years ago • Rao,Xiayu
like:
"error in round(x, digits): non-numerical argument for mathematical
function"
As I am using limma for the first time I am not sure if there is a bug
or if I did something wrong. Here is what I have tried.
I use the data set GDS1036...interested in comparison
between treatment and control and time points (see below).
>library(limma)
# read data table, rownames contained in first …
P2 |
+------+-----+
| ... | ... |
+------+-----+
So far I have always used the limma package in R here, but I have problems defining the study design for the repeated measures.
group <- factor(targets$time
updated 7.5 years ago • Gurkenkönig
<div class="preformatted">You seem to have a major problem with your analysis, which is that you
don't seem to have incorporated the dye swaps into your design matrix
at
all. You define a vector call 'vector', but then make no use of it.
Perhaps
you should investigate the use of the functions in limma such as
modelMatrix() which use targets frame to construct design matrices.
As far as the…
15:04:26 +0200
> From: "Jakob Hedegaard" <jakob.hedegaard agrsci.dk="" at="">
> Subject: [BioC] Limma - using both array and spot weights in lmFit
> To: <bioconductor at="" stat.math.ethz.ch="">
> Message-ID:
> <ea09c4b2b0f16e44b8f3311629493c0d0346e77c...This is much
better than hacking the weight matrix. See the Weaver case study
(Section …
div class="preformatted">Dear list members,
I am analysing my microarray data using limma package. Now I encounter
several problems. Looking forward to your suggestions!
Question 1:
During the process of background...step?
Thanks!
Dejian Zhao
++++++++++++++++++ Program Starts +++++++++++++++++++++
> library(limma)
> library(statmod) #duplicateCorrelation requires this packa…
updated 18.4 years ago • De-Jian ZHAO
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