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 …
Order by: Relevance
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
Hi there,
I am writing because I am lost in the last step after use limma::removeBatchEffect and introduce the new matrix to DESeq2. The reason I used limma::removeBatchEffect is because the...effect look correct.
Please, see my code below:
> library(DESeq2)
> library(limma)
> dds <- DESeqDataSetFromMatrix(countData = as.matrix(counts),
&am…
updated 5.3 years ago • Patricia
In one article, they used limma to fit a regression between each gene in their mRNA data with a specific protein expression. They report associated...genes with that protein as log2FC. here is my question.
1. How is limma handling a continuous variable in the model.matrix(lets LKB1 expression)
2. How is the logFC calculated for each gene
updated 17 months ago • adR
bioconductor at stat.math.ethz.ch" <bioconductor at="" stat.math.ethz.ch="">
> Subject: [BioC] [limma] Separate Channel Analysis of 2 color data
with
> summarization
>
>
> Dear List,
>
> I am analyzing some yeast Nimblegen...arrays following the separate
channel
> analysis of 2 color data of the limma package. After within and
be…
updated 15.4 years ago • Gordon Smyth
22:23 -0700 (PDT)
>From: Srinivas Iyyer <srini_iyyer_bio at="" yahoo.com="">
>Subject: [BioC] Limma: How to read gene list , coordinates of sport
> when NO GAL file available
>To: bioconductor at stat.math.ethz.ch
>...gt;Dera group,
>limma is an excellent module for gene expression data
>preprocessing and analysis.
>however, I …
updated 19.7 years ago • Gordon Smyth
I am running a microarray analysis using limma containing some spike-in controls that allowed me to know that I got a linear signal response with a data$E >= 2.3, where
updated 9.6 years ago • arfranco
It is easy to extract ordinary t-statistics from limma, as well as the
moderated t-statistics. It is explained in Section 8.1 of the User's
Guide -- do a text search for "ordinary.t...gt;
>This is fantastic because I can basically just copy and paste the
>instructions from the limma userguide.pdf document to get my
>differentially expressed genes.
>
>However, I …
updated 3 months ago • Gordon Smyth
comparing 2 by 2 these groups using for instance
LPE or another test like this one, option (2) using Limma.
What would be the best option ? I like using LPE since it is well
designed for low replicates. If I use option (1) should I normalize
and intuitive understanding of how empirical Bayes moderation (conducted by `eBayes` function of the `limma` package) in the `limma` analysis pipeline works. I tried to read through the [original paper](https://www.degruyter.com/document
updated 4.5 years ago • Junghoon
asubset of
data
from the normalized data, and
use it for the subsequentdifferential test in Limma.
Below is the script that I used for doing the cross-
arraynormalization,
averaging of in-slide technical
repeats, differential...test andmultiple testing corrections in package
Limma:
#Cross-array normalization
library(limma)
quantnorm_r<-normalizeBetweenArrays(normdata,method="Rquantile")
#…
updated 14.8 years ago • Arthur SHEN
Dear All,
I would like to ask about using the voom-limma workflow on RNAseq data. Usually, when I run the workflow, the samples contain similar number of reads (translating into...4-5.5M reads, with 2 samples having approximately 26M reads each.
My question is whether the voom-limma workflow will be able to "deal" with such a situation of such different amounts of reads or would this skew t…
I am working on TMT-labelled proteomics data (3 conditions in triplicates). Looking at the mean-variance relationship of my data on the peptide-level, it appears to be in good agreement with an additive-multiplicative error model, so I used vsn2 to transform the data. Now that the variance is stabilized, I believe I could directly use limma to asses the significance of changes on the peptide leve…
I have recently obtained very promising results using the diffSplice and diffsSpliceDGE from limma/edgeR, respectively. I was surprised to find that neither method has a cited reference despite being included in both...the main limma paper and both edgeR and limma user guides. DEXSeq in comparison has a separate reference in addition to DESeq/DESeq2...topSliceDGE.
As far as I can tell, diffSplic…
updated 9.4 years ago • maltethodberg
Hello!
I have load my RGList in Limma to start analysis but when I want to apply some functions (for example: plotMA3by2) R shows the error: "Error in E - Eb : non-numeric
Is there any need to set up a design or contrast matrix using limma ebayes on ratiometric replicates? I have three replicate ratios that are log2 transformed. I'm running ebayes
updated 8.2 years ago • reventropy2003
Background:**
I am comparing 6 colorectal tumor samples to 19 Normal samples using limma-RNASeq. I followed standard steps as suggested in the limma manual (hence not printing the code) to predict differential...Although for the most part DEG analysis worked, there were some unexpected results. For example, Limma predicted a set of genes that belong to a gene family called "CEACAM[1-5]", which ar…
updated 3.4 years ago • ACTG_&_beyond
hello,
i am new in microarray data analysis using limma package. when i am running command line given in tutorial their is error occur and i am not able to solve it. i have consider
updated 8.1 years ago • au.rinki.bio
to check wether batch exists then split the matrix into training set and test set.
Second, use limma to find different genes or windows in training set.
Third, select important features in different genes and windows...in test set.
However, in step1, t-SNE plots showed that there was obvious batch effect. limma could handle 'batch' by including batch as a covariate in a design formula f…
updated 4.4 years ago • hxlei613
gene symbol. So there about near 2000 duplicated genes. Generally, these genes were removed by limma::avereps. But I noticed that the author of DESeq2 mentioned that "not normalized countscould be feed into DESeqDataSetFromMatrix...So I wonder whether limma::avereps conducted and then round, or round before limma::acereps could be suitable feed into DESeqDataSetFromMatrix...Any suggestions would …
updated 3.5 years ago • Yang Shi
<div class="preformatted">Dear List,
I have question about using weights, avereps and lmFit in limma.
I've set weights for each spot using Flags from GenePix files.
Then I normalized data and removed control spots.
Next I...div class="preformatted">Dear List,
I have question about using weights, avereps and lmFit in limma.
I've set weights for each spot using Flags from GenePix file…
others on this list that this
>would be similar to randomized block model that's implemented in
limma
>(section 10.3 of the limma guide).
>
>See
https://stat.ethz.ch/pipermail/bioconductor/2004-December/006998.html...gt; > Sent: 20 January 2005 16:48
> > To: bioconductor
> > Subject: [BioC] Using limma with contrast matrix ,replicate
…
I am trying to run edgeR and limma for very high sample sample size groups (group1 sample size = 236 and group2 sample size = 490). The glmQLFit() in edgeR and...I am trying to run edgeR and limma for very high sample sample size groups (group1 sample size = 236 and group2 sample size = 490). The glmQLFit() in edgeR and voom...lmFit() in limma-voom takes about 2 min when using two confounding var…
2005 10:53:45 +0100
> From: Bj?rn Usadel <usadel at="" mpimp-golm.mpg.de="">
> Subject: [BioC] Limma two group layout; two approaches but different
> results
> To: bioconductor at stat.math.ethz.ch
>
> Hi all,
>
>...Refering to section 8.4 of limmas User guide (2 groups) I found a
little
> inconsistency (which might be a fe…
<div class="preformatted">Dear Biocondctors Users and Developers,
In a few days a go I send to this list a question about a design
experiment.
I receive suggestion about that design in two way: the first
suggestion
indicated that design was a 2-way factorial. The second suggestion
advice me to analyse it in limma and send me a script.
I start to learn about both suggestions. But, I see t…
www.stat.psu.edu/~zhao/bcc/respapers/AltmanInterface04.doc
but currently it does not discuss the limma implementation of this.
--Naomi
At 06:21 AM 12/9/2005, michael watson (IAH-C) wrote:
>Hi
>
>I would like to respectfully request...for complex (ie involving more than 3 samples) loop
>designs using two-colour microarrays in the limma documentation.
>
>…
Edit: this was in answer to https://support.bioconductor.org/p/56536/
Hi Richard,
In principle, they can be used in any combination, but the effectiveness of this awaits careful testing. I would personally be reluctant to use lmFit(method="robust") with the other methods just because I don't trust the variance estimators from the MM regressi…
updated 9.6 years ago • Gordon Smyth
Hi all,
I have an intercept issue that I do not understand with limma.
Let's say that I have a simple model with one group 'cancer sub-type' which contains 4 factors (TNBC, NonTNBC, HER2, Control
Hello,
i want to perform a DGE with data coming from a microarray experiment. My data is already normalized and i am looking for a way to feed it into the limma pipeline.
Is there a convenient way to transform my normalized expression dataset into log expression values and an...microarray experiment. My data is already normalized and i am looking for a way to feed it into the limma pipeline…
updated 3.4 years ago • waltheja
div class="preformatted">Hi,
I've performed a limma analysis on paired samples that were run on
Illumina
HT12 arrays, with three replicates in each condition. I'm a bit
troubled...7.5348228063 7.4471358372
7.2166929547 8.5194146676 8.0806964199 9.3741127592
I'd assumed that limma would have been more sensitive to this and am
wondering if anyone could please explain why this may be occurring…
id1=6&id2=48&id3=319
http://www.probes.com/media/publications/394.pdf
As far as I know Limma accounts for dye bias during normalisation. If
there is less/no bias will there be artifacts introduced? Or other
points
Hi,
After using SAM for a long time, I have started an "struggle" with the
exceptional LIMMA package.
After working with the example datasets and looking at the mailing
list, I have begun to analyse our own data
My data is qPCR
data,
analysing 92 protein markers in 92 samples (two groups). I would like
to
use Limma package to identify differently expressed genes between two
groups. The first 38 samples were controls, and the other
div class="preformatted">Hi,
I'm using limma package to do differential expression analysis on a
microarray data. May I know how the logFC is computed in the package
Hi all. Currently I am working on differential gene expression analysis using limma R package. The metadata of my dataset includes both Treatment and Time variables. Example of the same is shown below...Hi all. Currently I am working on differential gene expression analysis using limma R package. The metadata of my dataset includes both Treatment and Time variables. Example of the same is shown b…
updated 3.8 years ago • manju
preformatted">Dear list
I wonder if someone could help me with some conceptual issues
regarding limma, contrasts and analysis of an affymetrix study.
I have 8 samples (in duplicate) and 3 factors. The factors are O2
level (Norm
<div class="preformatted">
Hi!
I have a pretty odd (and lengthly to describe) problem involving
plotMA
(from package limma) and Sweave: Inside a Sweave document I want to
plot
4 MA-plots in one plot device. After the first two plots I set the
weight of all control spots to zero in order remove them from the
plot.
To my surprise, the changed weights appear to have a magic effect on
…
updated 17.6 years ago • Philipp Pagel
but, can anyone help me with a command,
that will export the normalised expression values from Limma (two
colour
experiment).
I have been previously been using an "average" function created by the
bioinfo person that was
I'm entirely new to limma/voom and the wider differential gene expression analysis field.
I have an experiment consisting of 20 patients, 7 time...design so far is:
mm <- model.matrix(~0 + timepoint)
But it's not clear to me from the limma manual how to use `duplicateCorrelation()` or exactly what it is doing. I assume it's needed in order to account for the variability
updated 3.9 years ago • annaschumannuni
I have a general question on running limma-voom on an RNA-Seq study with repeated measures.
I have a repeated measures design, where 19 subjects were measured over...subject" as a separate factor in the design matrix. However I am interesting in also applying the limma approach to allow the "subject" impact to be modeled as a random contributor; the impact of "subject" is not really of intere…
Hi
I am trying to specify a nested design for analysis with limma and having some difficulty.
For each subject in the study there are two tissue compartments measured. Within each tissue...Hi
I am trying to specify a nested design for analysis with limma and having some difficulty.
For each subject in the study there are two tissue compartments measured. Within each tissue, there are …
updated 6.3 years ago • Finn
<div class="preformatted">Dear list members,
My question relates to processing of Agilent single-color arrays. With
data generated using Agilent's feature extraction software.
My script so-for is mentioned below.
The flag information contained in raw data files is transformed to
weights. I have used 1 for 'good' and 0 for 'bad' in myFlagFun.
If this weight information is loaded:
-where do…
<div class="preformatted">Dear All,
I am using the LIMMA package to create 2 contrasts for my data and
then calculating the vennCounts of the decideTests from the
contrast.fit to be able to create venn Diagrams.
The code works fine but the summary(results) shows zeros for all i.e.
no gene were up regulated or downregulated. This is not true for my
data since toptable output shows Log fold …
a (nearly published) R program to bundle the features of many R packages for informatics, including limma and plsgenomics packages. I have come to rely on the complex program primarily for something much simpler than intended...which is extraction of significance testing from limma and plsgenomics. In the case of limma, I take a file which assigns a p-value to each feature (row). In the case of p…
updated 11.0 years ago • chandlerjd58
case that relies on no external data __and generates a scatterplot.
<pre>
require(limma); require(edgeR) # edgeR is for DGEList
set.seed(1234)
counts <- data.frame(matrix(as.integer(10*rexp(9*50)), ncol=9))
colnames...c("INTERCEPT","DrugX", "DrugY")
<span style="background-color:Yellow">contrast.mat <- limma::makeContrasts(DrugX…
updated 7.3 years ago • alexgraehl
38 +0100
> From: "michael watson \(IAH-C\)" <michael.watson@bbsrc.ac.uk>
> Subject: RE: [BioC] LIMMA - No residual degrees of freedom in linear
> model fits
> To: "Ankit Pal" <pal_ankit2000@yahoo.com>
> Cc: bioconductor...plain; charset="us-ascii"
>
> Well the computational aspect of it is simple.
>
> The limma c…
probe<-topTable(fit2,adjust="BH",coef=???,num=Inf)
try to run interaction model using limma but not sure if this is the right approach and what to mention in coef????
Thanks for your all help
updated 22 months ago • Jitendra
this is extremely suboptimal.
My question is, can I get meaningful results using voom (followed by limma analyses) if I set library sizes to 1000000? Intuitively this seems to make sense, since the TPM values are per million
updated 4.9 years ago • RJM
I would like to analyze RNAseq with 6 conditions using limma/voom. I have 6 biological replicates for control, however for the other 5 conditions (say C1,C2,C3,C4,C5) I have no replicates
in expression between normal and diseased subjects, regardless of time-point.
Using the LIMMA user guide I have used sections 9.5.2 and 9.7 to guide me.
Questions:
1. Looking at the code I wrote below, I have a feeling...disease 0_months
3 disease 3_months
...
#From 9.7 in the LIMMA user guide
Treat <- factor(paste(targets$Condition,targets$time_point…
updated 4.6 years ago • Chris
4112F human whole genome
microarrays
(with 45k features). Statistical analysis is performed using LIMMA
2.10.7 on
R 2.5.1.
Background correction was performed using normexp with an offset of
100.
Loess normalization was...a higher
variability into the measurements)?
* I already read in a reply by G.K. Smyth ([BioC] limma Normalization
question) that loess normalization might get problematic when…
updated 18.2 years ago • Serge Eifes
I'm using limma for the first time. I have a problem in creating a design matrix. I'm interested in finding genes that are differentially
updated 10.0 years ago • Linda Chaba
Hello Bioconductor Gurus!
(I apologize if this goes through more than once)
We are currently using limma (through the voom() function) to analyze
RNA-seq data, represented as RSEM counts. We currently have 246
samples
(including
for 400 samples. One way to do it would be by
simple correlations (Spearman CPMs) or by using limma (faster than
edgeR and DESeq for this task) and model the voom-transformed data as
Gene1 ~ Gene2.
The problem I see with the
Hello ,
I am currently working on 30 Affymetrix arrays for a time course
experiment using Limma package. I have two groups (A and B) with
samples taken at 0hr, 1hr, 6hr, 12hrs and 24hrs.
The following is how my targets file
for complex (ie involving more than 3 samples) loop
designs using two-colour microarrays in the limma documentation.
Although section 20.5 does give an example, with 5 RNA samples, one of
these is a pool which makes an obvious
div class="preformatted">The limma package has a new function topTableF() which ranks genes by
F-statistic.
I am planning to add a feature to topTable() to access
Recent ...
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