Error( subject / (treat *
task)
), rma_norm )
Now, I would like to translate the above model into LIMMA. I was bale
to do
run LIMMA without the error term. How can I include the error term in
LIMMA?
I greatly appreciate your suggestions
Order by: Relevance
I am analysing Affy chip data for differential expression. Previously
I have
done this using the 'limma' package without weighting the data. More
recently I
have been assessing quality control using the weights from the...in the subsequent analysis.
Does it
make any sort of sense to feed the affyPLM weights into the limma
lm.series
analysis? Alternatively, is there some way to use the limma eBaye…
gt; Cc: bioconductor <bioconductor at="" r-project.org="">
> Subject: Re: [BioC] about limma linear models
>
> Thank you for your reply. actually I have two biological replicates
in
> my experiment, and I'm confident...with the statistic power of limma
with
> your information.
>
>
> gang jiang
>
>
>
>
&g…
updated 14.6 years ago • Gordon Smyth
<div class="preformatted"> Hello everyone.
=20
I am currently evaluating difference between one-color and two-color
hybri=
dization to decide which one should be used for upcoming project. For
2-col=
or, I found in my self vs self hybs, the gene-specific cy5/cy3 bias
(i.e., =
reproducible red or green spots on self-self slides) is quite
significant. =
This will affect the real sample-contr…
updated 22.6 years ago • leon ding
div class="preformatted">Hi to all,
I've a doubt about Limma Package when working with log-ratios (M
columns
from MAList object) as input data.
As I don't have A columns, Can I perform
div class="preformatted">Hello All,
I want to create a linear model using limma design =
model.matrix(data$Time
* data$Tissue * data$Type) but i want Time to be a numeric one.
Any help?
[[alternative HTML version
div class="preformatted">Dear Group,
does limma provide gene set enrichment through a
wilcoxon rank sum test?
I overheard someone discussing that enrichment scores...provided through this method (limma - wilcoxon rank
sum) are better than GSEA enrichment scores.
I see some old 2005 tutorials usings Dr. Smiths gene
set test...to find any vignette that
discuss Gene set test and wilcoxon rank …
ran SAM on this data set. There is almost no overlapping
> between top genes picked up by SAM and limma. What could this imply?
Most likely that you have fit a different model in SAM. In my
experience
you don't get wildly different...results from SAM and limma, but it
might
not be obvious how to do the same analysis using the two different
tools.
>
> 3. It seems that lmFit …
updated 19.9 years ago • James W. MacDonald
div class="preformatted">
Hi,
I need help with analysis using the limma package. Here is the
experiment design:
20 patients, 10 on a regular diet and the other 10 on a special
treatment diet. For...both before/after treatment and day1/day6. I am at lost as how to
create a design matrix and call limma for such a study design. Can
someone please help?
Any input will be highly appreciated!
Yi…
<div class="preformatted">I had a question about how limma handles dye swap experiments.
The way we typically run these experiments is to label an aliquot of a
test set of (amplified) aRNA with Cy3 and another aliquot of the same
aRNA with Cy5. We do the same with the control aRNA and hyb opposite
dyes on two slides (i.e. slide 1: test Cy5/control Cy 3, slide 2: test
Cy3/control Cy 5). I…
div class="preformatted">Hi list,
I have some questions about using new version of Limma
and/or R.
I have read that the last version of Limma have
changes about reading GAL files. I am working with
several input...I need to read necessarily a GAL file, I don?t have
problems with the R version showing below and Limma
1.8
platform i386-pc-mingw32
arch i386
os mingw32
system i386,…
div class="preformatted">Hi,
I have a question about evaluating dye effects in limma.
In chapter 8.1.2 of limma users guide, an example is given to
demonstrate how to estimate dye effects. The design matrix
div class="preformatted">Thanks to help from Isaac Mehl, limma now supports ArrayVision data.
The
support is in limma 1.1.12.
The data file attached by Isaac is read by
read.maimages
15/09/2004, Fangxin Hong wrote:
>Does anyone know how to model interaction (two-way ANOVA) using limma
>package (lmFit)?
There is an essay on this topic in the section "Special Designs" in
the new
Limma User's Guide, available...from
http://bioinf.wehi.edu.au/limma/usersguide.pdf. If you wait a few
days,
this new material will be in the Bioconductor version of limma.
>Also,…
Hi all ,
how I can fix the following problem with package(limma) in R ??
<pre>
> biocLite("limma")
BioC_mirror: http://bioconductor.org
Using Bioconductor version 3.0 (BiocInstaller 1.16.5...R version 3.1.3.
Installing package(s) 'limma'
trying URL 'http://bioconductor.org/packages/3.0/bioc/bin/windows/contrib/3.1/limma_3.22.7.zip'
Content type 'application...zip' length 4628…
updated 10.1 years ago • libya.tahani
ve extracted my summarized data from aroma.affymetrix as a data
frame,
I now need to import it into limma and normalize to the 0h time point.
My ultimate goal is to return a gene list and heatmap that pass my
filters, say p<=.05...and fc>=1.5
My main question however, is if there is a function in limma or any
other package that will perform this normalization to the 0h time
point
a…
updated 17.5 years ago • Roberts, Raymond
and healthy. I can get the contrasts between healthy and disease
comparisons using contrasts in LIMMA. But here each disease has 2-3
arrays from different patient blood samples. These are not true
replicates, per se but thats...all we have. My question is how do we
treat them? Can I consider them as replicates? (I understand LIMMA
will
combine the replicate data.)
here is the design........
1. di…
div class="preformatted">
Hi
trying to use limma with my own genepix data
have a problem when I try to use the following commands:
> dictyMA <- normalizeWithinArrays...makes sense)
presuming of course that -1, 1 correspond to the order in which you
have
read them into limma in the first place ?
thanks
Jason
--
--------------------------------
Jason Skelton
Pathogen Microarr…
four columns of log2-transformed ratio data
(http://ifile.it/ija65rq).
I want to analyze it with LIMMA, but stuck with duplicateCorrelation:
> library(limma)
> M <- read.delim('M.txt')
> design <- cbind(c(-1, 0, -1, 0), c(0, -1, 0, -1))
> corr
experimental conditions.
Which
means that the normalisation is done by factors in the ANOVA model
limma is much used for the first approach, whereas I think Maanova is
more
used for the second approach.
Does anybody have any...experience on both approaches? WHat is
recommended?
Can the limma package be used for the second approach?
Additional question: Can continuous covariates be fitted with …
<div class="preformatted">Hi all,
I've been struggling a bit with GEO and limma. I've come up with 2
questions that I'ld appreciate some input on.
Question 1:
I have a design matrix with 6columns for an expression set with 3
columns(3 levels, 2 agents). How do I create a model matrix to fit my
design matrix for this dataset (eg. gds3715 below)? For a straight
forward single factor analysi…
div class="preformatted">Hi all,
Although limma-voom seems to give us really good results in our RNA-
seq experiments, we still have some doubt about y$E values (i.e.
expression...function (default option). I need a
clarification here: it has been explained many times that limma (and
edgeR too) do not need to take into account gene length as they
perform gene-wise statistical tests: feature le…
updated 12.9 years ago • Cittaro Davide
div class="preformatted">I have committed a new function avereps() in the limma package on
Bioconductor. It is somewhat slow, but will handle irregularly spaced
spots. I have committed it to both the...release and developmental
branches
of Bioconductor.
If you re-install limma from Bioconductor in a couple days you should
be
able to use it.
Best wishes
Gordon
On Tue, 3 Jun 2008, Erika Mel…
div class="preformatted">Dear mailers,
I am interested in using Limma to analyze my single-color Agilent
microarray data. Before that, since I am new to Bioconductor/R/Limma,
I
just wanted to...me
in
this regard.
1) I have TIFF images scanned using Agilent Feature Extraction
software. Can Limma accept TIFF images and work on it? or it will
only
accept txt files?
2) Can Limma produce an out…
updated 13.9 years ago • Karthik K N
before and I did not pay enough attention to. My question is if there
is a
textual description of limma, just like affy or other package?
Your help is greatly appreciated!
Thanks,
wenqiong</div
div class="preformatted">Hi,
I am attempting to process a few Agilent 4x44 based arrays using
limma. When I try to estimate expression levels with lmFit in limma, I
get the following message:
Warning message:
In lmFit(MA
div class="preformatted">Dear BioC,
I'm trying to make use of the "makeContrasts" function in "limma", but
I
am getting errors. Where do I go wrong? First a little background
info:
I have 3 different ages (18, 25 and 29 days) en they...unconnected design. So I tried to use
Chapter 9 (Separate Channel Analysis of Two-color Data) of the limma
User's manual. When I try to make a contrast, I am …
div class="preformatted">Hello, all
I am using Limma for my array analysis. Based on the user's guide, I
canconvert B value to probability.
however, in my results, I have adj.P.Val
<div class="preformatted">Hi limma Users,
I did a contrast in our analisis like this:
(mutant treated-mutant control)-(wildtype treated-wildtype control)
We...div class="preformatted">Hi limma Users,
I did a contrast in our analisis like this:
(mutant treated-mutant control)-(wildtype treated-wildtype control...are interested in to known what "M" value means in this situation?
In l…
<div class="preformatted">Hello,
I have cDNA, I tried limma to do normalizeWithinArrays, but the
results looks
like they did not aveage spots. Each spot was printed twice in my cDNA...div class="preformatted">Hello,
I have cDNA, I tried limma to do normalizeWithinArrays, but the
results looks
like they did not aveage spots. Each spot was printed twice in my...array,
how limma average the…
div class="preformatted">Dear Endre,
It sounds as if limma recognised the ArrayVision format fine. As far
as I
know, there is no way to tell from the ArrayVision file which channel...is
cy3 and which is cy5. Even though limma got them the wrong way around
in
this case, it doesn't really matter because it makes no difference to
the
analysis. The...gt; From: "Endre Sebestyen" <endre.sebes…
div class="preformatted">Dear Limma users
After finishing the analysis successfully with replicates, I am now
trying to analyze the same without replicates...After following a
suggestion that I can use Limma without applying the fit2 <-
eBayes(fit2) step (for without replicates), I tried to do the same for
just one of the patients...fit2 <- eBayes(fit2) step because of lack of r…
two classes and paired experiments I have been
using a paired t-test. However, I would like to use
limma with my arrays. Somewhere, I found that I could
introduce a block in order to get the lmFit. I have
been doing that for a while...and getting pretty nice
results. However, recently in the new limma manual
appears that the block option should be used for
technical replicates, and you need to ca…
08:14:53 -0500 (CDT)
> From: jihoon at cs.wisc.edu
> Subject: [BioC] p.value in eBayes( ) of limma
> To: smyth at wehi.EDU.AU
> Cc: bioconductor at stat.math.ethz.ch
>
> Dear Smyth,
>
> Hello,
>
> I'm curious about...degree of freemdom is used)
> from the R example of the function lm.series
> in the package "limm…
div class="preformatted"> I've been examining the eBayes function in Limma using some
affymetrix data
we have. The default proportion setting: 0.01 I think is probably
wrong for
the comparison
<div class="preformatted">Dear Koen,
This bug was introduced last week in limma 2.9.10 with an attempted
cleanup
of the read.maimages() function. I've committed a fix in limma
2.9.11.
Best wishes
Gordon
>[BioC] read.maimages broken (limma 2.9.10)?
>Koen Bossers k.bossers at nin.knaw.nl
>Fri Feb 16 12:20:57 CET 2007
>
>Hi,
>
>I seem to be …
but I am trying to use R to do proteomic analysis. Raw data is normalised and I am trying to use limma to create a DE table. Code has worked previously for a colleague but I can't seem to get limma to run.
Tried
```
if (!require("BiocManager...install(version = "3.19")
```
which I used to install BiocManager which works.
To install Limma have tried
```
install.packages("limma")
…
updated 16 months ago • Jennifer
Dear list,
I got a considerably different log2 Fold change with ordinary limma-voom and weighted limma-voom.
Am I correct that for weighted limma voom the log2 FC is
log2 FC=
average over experiment...samples of (sample.weight*log2((counts+0.5)/(total.counts+1))/norm.factor)))
and for unweighted limma-voom log2FC = the same quantity without the sample weights?
If so, I calculated bo…
results" which doesn't necessarily exist.
Right. Thanks for pointing this out. It has been fixed in limma 1.8.10
(available from http://bioinf.wehi.edu.au/limma or from CRAN).
Cheers
Gordon</div
<div class="preformatted">Dear Dr. Gentleman and Dr. Davis,
Thank you very much for the informative explanation. It is nice to
know
that limma is somewhat an (positive) outlier.
Regards, Adai
On Mon, 2005-02-28 at 04:57 -0800, Robert Gentleman wrote:
> Hi,
> Bioconductor has a release version (just as R does) and that
remains
> relatively static through its life, …
<div class="preformatted">Dear Sir
I am a novice to limma. I meet some questions and can't solve
these by
myself. So please give me a hand.
firstly, I wonder could I use two wt.fun to filter bad spot, for
example:
myfun1 <- function(x, threshold=50) {
+ okred <- abs(x[,"F635 Median"]-x[,"F635 Mean"]) < threshold
+ okgreen <- abs(x[,"F532 Median"]-…
updated 20.5 years ago • ? ?
Sir/Madam,
The bioinformaticist whom we cooperated with analyzed the Agilent
microarray data with LIMMA and Genespring. As what she said, LIMMA
should be more stringent than Genespring, so that we can get more
genes with Genespring...is:
1 Is this kind of situation reasonable?
2 What' the reason for the different results between LIMMA and
Genespring?
Best wihses!
Ming
________________________…
updated 14.1 years ago • Jin, Ming
<div class="preformatted">Hi,
I've a problem using limma with bluefuse output files (I've saved
those files as .xls)
I'm able to use one file per time without any trouble but when I...div class="preformatted">Hi,
I've a problem using limma with bluefuse output files (I've saved
those files as .xls)
I'm able to use one file per time without any trouble but when...more than
one file usin…
div class="preformatted">I've committed a major bug fix to the treat() function of the limma
package. Users of this function should re-install limma 2.18.2 or
2.19.2
from Bioconductor.
I've introduced a new function
could in principle have been Inf,
meaning that 0*NA can't be inferred to be 0.
You could argue that limma should assume that infinite expression
values are impossible, therefore it should treat 0*NA as 0, but I
haven't so far...the effort.
In your example, you could get the contrast you want without NAs
simply by telling limma explicitly that the 3rd coefficient doesn't
appear in your contrast,…
hi
I am using LIMMA to identify DEGs. I got the top 5 DEGs. But i am not able to get the whole list of DEGs with proper id and genes.
Here i used...the code
write.table(topTable(fit, coef=1, adjust="fdr", sort.by="B", number=500), file="limma\_complete.xls", row.names=F, sep="\\t")
 
updated 9.1 years ago • mathavanbioinfo
variable.
I would like to look at the whole set of genes and for that I would
normally use limma, but limma has the expression level as the response
variable and so the binary outcome would be an explanatory variable
updated 15.8 years ago • Daniel Brewer
should use the measurements of each channel separately
rather
than using the channels ratio. In limma, after normalizing, we left
with
M and A values and if what I described above is correct I don't
understand how to analyze...loop design in limma.
Is there a way to get the normalized channels rather than the
normalized ratios?
Thanks,
Ron
[[alternative HTML version
<div class="preformatted">Hi everyone,
I am not a statistician, so please forgive me if my question is
trivial.
I have some difficulties with the factorial design in limma with 2
factors with 2 and 3 levels respectively.
Say the two factors are "Treatment" and "Source", with respectively
two
and...please forgive me if my question is
trivial.
I have some difficulties with the factorial des…
Hello list
In the recent limma paper (Nucleic Acids Research 2015) it was mentioned that limma is applicable for analyzing Nanostring data.
I have nanostring...analyze them. The data can be treated as regular digital counts (RNA-seq) and be analysed using voom-limma approach. Alternatively I can apply the normalization steps recommended by the company (<span style="line-height:1.6.…
updated 10.7 years ago • mali salmon
read.maimages from limma with a "broken" file (tabs
replaced
>by ":", two extra tabs added at the end of row e)
>limma reads the table fine
>
>table:
>...delimiters at the of the end of the lines being ignored.
Perhaps I will add flush=TRUE to the limma read by default.
>Marray on the other hand, complains using the following syntax and
>refuses t…
<div class="preformatted">Item Type: Appointment
Begin time: Mon, 02 Oct 2006 05:00 pm +0000
Duration: 1 Hour
Location:
Hi,
I've a problem using limma with quantarray output files. I've changed
all output files to ANSI format, because the original Unicode format
is not accepted by limma.
I'm able to use one file per time without any trouble but when I try
to load more than
one file usin…
Mark Pinese <z3062573 at="" student.unsw.edu.au="">
> Subject: [BioC] Significant dye bias using limma
> To: bioconductor at stat.math.ethz.ch
>
> Hello all,
>
> I have some questions regarding whether the significant...m
finding in
> my analyses could be an artefact of my analysis method.
>
> I've been using limma to analyse a …
dye bias I'm
finding in
my analyses could be an artefact of my analysis method.
I've been using limma to analyse a simple design comparing treatment
and control
cases using dye swaps. As per suggestions in the recent...limma Users'
Guide,
I've added an intercept term to the design, and used it to find genes
with
significant dye effects. limma reports
We are testing limma-trend and limma-voom on simulated scRNA-seq data using splatter package. We tested low-depth, high-depth, sparse, and less...sparse data. In all cases, limma-trend surpassed limm-voom in F-score and precision-recall. Could you provide any theoretical ground for this difference
updated 3.1 years ago • hainct
div class="preformatted">Dear Sir/Madam:
Glad to writing to you.
I'm trying to use limma to analyse my microarray data. now I can
get the "MA.txt"file which contains all of the ratios and intensities.
but I want
updated 21.4 years ago • κ¸Õ£¨±±¾©-¶¯Ì¬»ù
<div class="preformatted">Dear Vanessa,
limma always assumes complete print-tip-groups, so the only way to
use imageplot() correctly is to complete your arrays by putting back
to last 4 spots of each print-tip-group as NA. You can do this by:
narrays <- ncol(RG_e1)
Y <- matrix(NA,21632,narrays)
RG <- new("RGList",list(R=Y,G=Y,Rb=Y,Gb=Y)
RG$printer <…
updated 18.3 years ago • Gordon Smyth
div class="preformatted">Hi,
I am using limma to analyse an experiment where I am comparing the
response in stimulated verses un-stimulated cells in individuals...by analysing data using fold change
only) and these genes have the highest ranked p values in the limma
analysis (although not significant when adjusted).
I have tried to filter the data set (to the 3000 most variable genes
updated 21.2 years ago • Anthony Bosco
2005 10:30:43 +0200
> From: "Ron Ophir" <ron.ophir at="" weizmann.ac.il="">
> Subject: [BioC] [Limma] Correcting Dye swap effect
> To: "<bioc <bioconductor="" at="" list"="" mailing="" stat.math.ethz.ch="">
>
> Hi,
> In Chapter 8.1.2...Limma users guide there is a description how to
> detecting the Dye effect.
> The example th…
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