My
question is, how would I incorporate the duplicate correlation aspect
when defining the design in limma?
Thank you for your reply and help.
Yolande
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Hi all,
I'm currently analysing a microarray dataset, on which I'm trying to detect the difference of gene expression between responders and non responders to a treatment.
Even after reading the Limma user guide and searching on the forum I'm not really sure which design matrix I should use for the comparison.
Here is a simplified model of my dataset :
cy3 cy5
…
updated 6.9 years ago • Guillaume Robert
<div class="preformatted">Hello,
I am hoping someone will be able to help me with this. I am analyzing
the two color common reference design agilent arrays using Limma. I
have four replicates and two treatments(control and PCB). I am trying
to extract fold change values (PCB/control) for the...able to help me with this. I am analyzing
the two color common reference design agilent arrays us…
<div class="preformatted">Dear All,
I'm have data txt files from Agilent's 60mer Arabidopsis slides that
were created using Agilent's feature extraction software, and am
trying
to read them into limma (using Bioconductor) and have encountered the
following problem.
I can read in my targets file just fine but with the follow...that
were created using Agilent's feature extraction software, …
Dear BC list,
I am using limma the first time.
I have an unbalanced sample with 4 type of individuals,
Healthy : 3 individuals
Treatment A : 10 individuals
updated 10.5 years ago • Gabin Pierlot
Good morning
I have a question regarding the function `removeBatchEffect` from `limma` package.
This is my experimental design
ID Patient Metastasis
S1 A NO
S2 A YES
S3 B NO
S4 B YES
S5 C NO
S6 C YES
S7 D NO
S8 D YES...gt; mydesign <- model.matrix(~ Patient + Metastasis, data = colData)
> vst_mat_noBatch <- limma::r…
updated 5.4 years ago • Pietro
Hello everyone,
I have some RNASeq data, that has been spiked-in with exogenous ERCC controls. I have the counts from htseq-count and now I want to normalize + test for differential expression. For this, I am using two methods: DESeq and limma+voom. Below is my code for both the tests. Can someone tell me if what I am doing is correct or not? I do think that I am slightly...to …
updated 10.2 years ago • komal.rathi
at="" yahoo.com="">
>From: Gordon Smyth <smyth at="" wehi.edu.au="">
>Subject: [BioC] Limma: How to read gene list, coordinates of sport
>when NO GAL file available
>Cc: bioconductor at stat.math.ethz.ch
>...0700 (PDT)
>>From: Srinivas Iyyer <srini_iyyer_bio at="" yahoo.com="">
>>Subject: [BioC] Limma: How to read gene l…
updated 19.8 years ago • Gordon Smyth
one cdf kernel to be Poisson and the other one to be Gaussian.
4. Then apply gsva scores to the **limma** package to fit a linear model by `lmFit()` function. Then select pathways with adjusted p value smaller than 0.01 to be gene...even some of them changed from positive to negative?
2. How to interpret the linear models in **limma** package. It has coefficients explained as fold change.…
<div class="preformatted">Dear Birger,
I just tried the code from the book on R 2.4.0 and R 2.5.0 and I was
not able to reproduce the error you are mentionning. My Bioconductor
installation on R2.4.0 is the following:
> sessionInfo()
R version 2.4.0 (2006-10-03)
i386-pc-mingw32
locale:
LC_COLLATE=English_United States.1252;LC_CTYPE=English_United
States.1252;LC_MONETARY=English_Uni…
updated 18.7 years ago • Paquet, Agnes
preformatted">This question is because I am misunderstanding how certain things fit
together in Limma. There is no example like this in the documentation,
and
I am trying to figure out how to do this based on examples section...the virus.
- Total of 8 donors
The question I have is how to deal with the ' donor effect' using
Limma.
First case (1): I could assume that my donor variability is muc…
fold change per gene from the microarray data. I'm working with agilent microarray data using the limma package. Question one is, is the normalisation afffected by the filtering and hence has to be done before? Question two...The raw object then looks like this:
<pre>
> str(raw)
Formal class 'EListRaw' [package "limma"] with 1 slot
..@ .Data:List of 6
.. ..$ : num [1:42303, …
updated 9.4 years ago • maximilian.collatz
Hi Guys
Rather an odd title, but here goes...
Basically I have read in my data in both limma (using read.maimages)
and marrayInput (using read.marrayRaw).
I want to normalize my data using loess normalisation
the replicates from different blocks this difference
is
entirely regular for all the genes.
If limma is applicable using all replicates as replicates I need to
sort my
RGList so that spacing = 1 applies without loosing
the standard method. Interestingly, however, when I used the ordinary standard deviation from the LIMMA analysis, I also get larger effect sizes for CpG probes in general (see table and figure below). I did not expect the results...fit2_D1$coefficients / (fit2_D1$sigma))```
**Figure:**
![Difference in effect size calculate by LIMMA (using ```fit$sigma```) and my function (see Snippet "cohensD_…
updated 4.8 years ago • MoltenLight
error
> 2) Multiple R-Squared
> 3) Adjusted R-Squared
> 4) F-statistic
>
> With limma, and eBayes, I deduce (incorrectly?) that efit$F and efit
> $F.p.value
> convey information similar to number 4 above. How
div class="preformatted">Hi,
I'm confused about creating a contrast matrix with Limma. I've got
three groups (LA1777_X, LA_1777_6, LA1777_LVS), each replicted
threefold. I would like to use the group LA1777_LVS
the samples appear closer than they
otherwise would.
>
> Further, when performing t-tests / LIMMA on the full data, those
genes that are close to background level should not contribute to
significant differences...file: HumanWG-
6_V2_0_R4_11223189_A.bgx, and I am normalising using the NEQC function
in the LIMMA package.
>>>
>>> I know there …
updated 12.5 years ago • Wei Shi
of the raw data.
For differential expression analysis I use linear models implemented
in
the limma package
as described in the vignette for one-color data.
Oddly enough these analysis always brings up genes which aren
updated 17.3 years ago • Christian Eisen
div class="preformatted">Hi Dear BioC!
I have a question concerning batch effect using Limma. I searched
through the BioC archives but didn't find the answer to my question.
Suppose I have the folling three factors
updated 17.5 years ago • Paul ChristophSchröder
<div class="preformatted">
Hi,
I am using the Limma package and I am getting warnings when trying to
fit a linear model to my data in an "MAList", using a vector of
weights (0 or...div class="preformatted">
Hi,
I am using the Limma package and I am getting warnings when trying to
fit a linear model to my data in an "MAList", using a vector of
weights (0
I have received extraordinary help on this website, and while I have learned a lot about limma, I am still a beginner and am trying to overcome certain limitations. I am trying to determine the effect of a condition
updated 8.8 years ago • gstone2
Hi, I'm making a rnaseq analysis using Limma, and I have a lot of samples. I trying to compute the design matrix and then the lmFit(). But when I call lmFit it returns
>...Hi, I'm making a rnaseq analysis using Limma, and I have a lot of samples. I trying to compute the design matrix and then the lmFit(). But when I call lmFit it returns
> coefficient
updated 5.6 years ago • Will
Bioconductor. Until now the only experience I have is in analyzing
microarray data using affy and limma packages. Now I'm trying to
analyze
Rat Gene 10 st arrays and I would like to run RMA analysis and Smyth
moderated t test...many of the questions and
responses on this mailing list, I decided to use pdInfoBuilder, oligo
and limma packages to run analysis.
I built my package according to info a…
updated 17.0 years ago • Anne-Marie Madore
each fragmented 12 times, with three replicates = 72 samples
total.
I found some examples from the limma user's guide and other materials,
but
I'm still having trouble.
http://www.bioconductor.org/help/course-
materials/2009...BioC2009/labs/limma/limma.pdf
https://stat.ethz.ch/pipermail/bioconductor/2012-January/043154.html
http://www.bioconductor.org/packages...2.12/bioc/vignettes/limma/inst/do…
updated 12.2 years ago • Lisa Cohen
Hi, using RNAseq I am interested in the RNA expression signature of two patient groups. Initial analyses with LIMMA indicate that there is a source of variation which contributes more to the variance within the sample groups than between...RNAseq I am interested in the RNA expression signature of two patient groups. Initial analyses with LIMMA indicate that there is a source of variation which co…
the performance of a model based on a fully Bayesian approach with the model implemented in the limma package. My data looks like this (protein-wise):
sub.1 healthy tissue.1
sub.1 healthy tissue.2
sub.1 healthy tissue.3...is the effect of interest
- epsilon_jlsi is the random residual
To adapt this model to limma package i reparameterized the model in this way:
…
updated 4.0 years ago • Giovanni
class="preformatted">Dear list,
I have a questing regarding the 'plotMDS' function in EdgeR (and
limma).
In my case the plot generated (see attachment) is hard to read, since
some of the labels are at the exact same place in the
```
>Date: Sun, 17 Jul 2005 12:05:41 +0200
>From: "Johan Lindberg"
<johanl at="" biotech.kth.se="">
>Subject: Re: [BioC] A question about paired data and how to set up the designmatrix in LIMMA
>To: <bioconductor at="" stat.math.ethz.ch="">
>
>Dear Bioconductor users.
>I posted a question a while ago that did not get an answer. I'm so…
analysis agnostic to location and cell type. Do I use a method originally designed for microarrays (limma) or one originally designed for RNASeq (edgeR, Deseq2, or voom). I would especially appreciate Gordon Smyth's input on this
<div class="preformatted">Hi everyone:
I have one microarray data set considering differentiation in a cell
line. About 7 time points for both control and treatment, no
replicates
I would like to use limma to find the differentially expressed genes
between time points for control and treatment, and want to compare the
gene...a cell
line. About 7 time points for both control and treatment, …
updated 13.8 years ago • Chunxuan Shao
div class="preformatted">Hi,
On the limma usersguide I found the example:
FileName Cy3 Cy5
File1 wt1 mu1
File2 wt1 mu1
File3 wt2 mu2
File4 wt2 mu2
where two wild
I now know how to get genes highlighted in a Volcano
plot based on p-values from the results of my limma analysis. I would
like to get a list of the genes highlighted. For example, the code
below gives me a volcano plot with the
<div class="preformatted">
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
between
arrays normalization steps I did a summarization (medianpolish of M
and A
values for...analyzing some yeast Nimblegen arrays following the separate
channel
analysis of 2 color data of the limma package. After…
updated 15.4 years ago • Ana Conesa
Dear list,
Just need some place to check my code for the analysis of my array
experiment using Limma. As I'm unsure and have a feeling I'm missing
something.
My experimental setup:
2 groups A and B of 6 samples in a common refrence
Hey! I'm doing some analyses with Limma. I have 5 cluster and I want to find genes up and down regulate in the first one versus the others 4, to identify the ones...Hey! I'm doing some analyses with Limma. I have 5 cluster and I want to find genes up and down regulate in the first one versus the others 4, to identify the ones that
updated 2.1 years ago • michelafrancesconi8
I have a question about averaging microarray probes of a given dataset. It seems like `avereps` of `limma` calculates the average for replicate probes. As soon as the missing values (NA values) are introduced the calculations
updated 2.8 years ago • mohammedtoufiq91
I have a question about averaging microarray probes of a given dataset. It seems like `avereps` of `limma` calculates the average for replicate probes. This is OK, as soon as the missing values are introduced the calculations
updated 2.8 years ago • mohammedtoufiq91
In limma manual, the example of time course experiment (Section 9.6) the target frame showed 2 replicates of 0hr wt and mutant...In limma manual, the example of time course experiment (Section 9.6) the target frame showed 2 replicates of 0hr wt and mutant but
updated 7.0 years ago • shuvadeep.maity
Hi,
I wonder if analyses of "non-linear"-like dose-response data is or could be covered by limma. By dose response gene expression data I mean data with 5-10 doses (3-5 biological replicates) of a chemical treatment...Hi,
I wonder if analyses of "non-linear"-like dose-response data is or could be covered by limma. By dose response gene expression data I mean data with 5-10 doses (3-5 biological…
updated 8.3 years ago • Pekka Kohonen
I've started to play around with limma's new wsva() function to generate surrogate variables. The help page says under Value: "Numeric matrix, same as design but
updated 8.2 years ago • Jenny Drnevich
A)
alone. I am not trained as statistician, so correct me if I am wrong.
I am trying to use Limma with design matrix of
1 0 0 0
1 0 0 0
1 0 0 0
0 1 0 0
0 1 0 0
0 1 0 0
0 0 1 0
0 0 1 0
0 0 1 0
0 0 0 1
0 0 0 1
…
Dear List,
Sorry for posting a very minor thing or if this has been posted
already,
using limma 2.2.13
I don't get ProbeIDs back when calling toptable
toptable(fit,num=1)
M t P.Value adj.P.Val B
22488 13.32117 197.5873
Should I be concerned about such extensive filtering? Does it affect
further analysis with limma and introduce bias? If it's a problem,
what are the available solutions or diagnostics?
Thanks for your help!
Best regards
updated 11.6 years ago • Guest User
Dear Bioconductors, I want to do something simple, which I cannot find
the solution to. I have a limma data frame and I want to select a
subset of the data frame based on whether the values in the "G"
channel are > e.g. 5000
like file using the column headers.
The following code used to work, but now is broken:
library(limma)
cols = list(Rf="F635 Median",Gf="F532 Median",Rb="B635
Median",Gb="B532 Median")
RG = read.maimages("mydata.gpr", columns=cols)
Is this...a bug? How can I get around this problem?
I have tried
limma version 2.7.8 and 2.7.9
I'm on a Mac OSX 10.4.7
Running R.app 1.16
The error message is:
E…
updated 19.4 years ago • Bobby Prill
8 replicates on the bovine genechip. I am attempting to
understand the
results that I obtain using limma and adjusting for fdr. I have tried
reading the help vignettes on p.adjust and topTablle but no closer to
understanding...lab
(by abstract) I know that I may need to use a less stringent fdr then
5%
but I am unsure in limma how to change that value (or if it is
feasible at
all). Looking at the…
updated 17.5 years ago • Louisa A Rispoli/AS/EXP/UTIA
library size, cell type composition).
At this point, I've controlled for these covariates using limma+voom, leaving me with residuals *r1* and *r2*. Since *r2* and *r1* have already been log transformed, I believe I can take the logFC...are there any other approaches you would suggest that might let me maintain the weights from limma+voom
Jul 2007 15:50:47 +0200
>From: "Serge Eifes" <serge.eifes at="" lbmcc.lu="">
>Subject: [BioC] Limma and randomized block design for time-course
> microarray experiment
>To: <bioconductor at="" stat.math.ethz.ch="">
>...time-point.
>
>Is it possible in this case (unbalanced design) to use randomized
blocks in
>LIMMA to…
updated 18.5 years ago • Gordon Smyth
Hi,
I have a bunch of genes wants to get gene-expression difference using Limma. In the output I would like to have Mean\_Case + SD and Mean\_Control + SD of each gene along with other parameters such as...Hi,
I have a bunch of genes wants to get gene-expression difference using Limma. In the output I would like to have Mean\_Case + SD and Mean\_Control + SD of each gene along with other parame…
div class="preformatted">Dear list,
I am not sure how to create the proper design in limma for my
experiment which I think is a factorial and paired combined.
I have 9 patients that are on 3 different diets (3 patients
Hi all,
could anyone please help how to design model in limma for categorical variables association with methylation epic array data?
I am using below model but keep getting error
updated 23 months ago • Jitendra
important factors implemented from the phenoData object. But one of my major concerns about using limma for more than one variable, is that one specific variable that i want to test regarding differential expression between
updated 11.0 years ago • svlachavas
Dear All,
I have shRNA dropout screen data obtained by using GMAP (Gene Modulation Array Platform): several cell lines, 2 time points for each, and for each cell line I would like to find the shRNAs that dropped out or at least significantly decreased across these 2 time points.
I was wondering whether limma package can be appropriate for such kind of data - just to perform differential express…
updated 9.6 years ago • Anna Dvorkin
Hello everyone,
It is my first post here. Today I've been asked to perform a Differential gene epression analysis between two groups of normal vs treatment.
The analysis was performed with an Illumina MicroArray.
Till now I've performed limma analysis using GES GEO files in quite a simple way, but today I've been ask to work on a file like this:
data.txt
```r
ID_REF Sample-A1 Sample…
<div class="preformatted">Dear Paul,
I'm not quite sure why you're so shocked about getting significant
results. Usually people complain to me when they don't get
significance
:).
limma is able to obtain much higher significance levels than a t-test
because it (i) leverages information from the within-array...about getting significant
results. Usually people complain to me when they don…
updated 16.2 years ago • Gordon Smyth
<div class="preformatted">Hi Sally --
"Sally" <sagoldes at="" shaw.ca=""> writes:
> Hi,
>
> I am using the current version of LIMMA (January 25, 2009) and am
> having the following error message from this script below:
>
> Error Message: Error in new("AnnotatedDataFrame...Sally" <sagoldes at="" shaw.ca=""> writes:
> Hi,
>…
B,D are
unaffected.
Noted some families have more than 1 affected or unaffected samples.
How does LIMMA take the two-level (technical replicate and familial
relationship)
dependence into account?
Can I just simply do this
<div class="preformatted">Unfortunately, we have become aware recently that the FC calculation
in Limma
Is not correct. We input the expression values as log2 transformed
values. The
Average log expression value is then calculated...div class="preformatted">Unfortunately, we have become aware recently that the FC calculation
in Limma
Is not correct. We input the expression values as l…
updated 15.0 years ago • Lana Schaffer
response ~ condition, data=mydata, random= ~1 |
Subject)
Is there something analogous to this in limma?
Cheers,
Rob.
</div
updated 20.2 years ago • rob foxall IFR
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