div class="preformatted">Hi,
-using Bioconductor v1.8.1 and limma v1.6.1
When I use backgroundCorrect(minimum) and then dupcor.series I don't
get
a correlation value (NaN), if I don't use...statmod
Attaching package 'statmod':
The following object(s) are masked from package:limma :
matvec vecmat
> cor$cor
[1] NaN
> MAdef=normalizeWithinArrays(RG, RG$printer)…
Order by: Relevance
analysis program? And how
can I can remove these bad spots from further calculation in R using
the limma package or any other functions in R?
Thanks,
Anna</div
Dear all,
I am confused about how t-test or F-test is implemented in limma/edgeR.
Let's say I have a small dataset: two conditions, each condition has 3 replicates, and there are 4 genes.
<table border...nbsp;</td>
<td> </td>
<td> </td>
</tr>
</tbody>
</table>
My questions is if I use limma/edgeR to analyze the DEGs…
div class="preformatted">Hello list,
Can LIMMA work with beta distributed interval(0,1) data? Thanks,
Steve
[[alternative HTML version deleted]]
</div
2008 10:56:13 +0100
> From: Daniel Brewer <daniel.brewer at="" icr.ac.uk="">
> Subject: [BioC] Limma: import files with genes missing
> To: bioconductor at stat.math.ethz.ch
> Message-ID: <48032A3D.20300 at icr.ac.uk...gt;
> Content-Type: text/plain; charset=ISO-8859-1
>
> I am trying to use limma to import a series of bluefuse post
pr…
updated 17.7 years ago • Gordon Smyth
<div class="preformatted">
Hi,
I used the CMA package (v1.0.0) to evaluate the performance of a
kNN
classification after a feature selection step using limma,
including the
whole procedure in the cross-validation.
Before finding the CMA package I had implemented myself the same
procedure
(cross-validation of feature selection) and I couldn't get the same
result
as wit…
updated 16.8 years ago • Renaud Gaujoux
file: HumanWG-6_V2_0_R4_11223189_A.bgx,
and I am normalising using the NEQC function in the LIMMA package.
I know there are traditionally a number of Illumina identifiers and I
am
concerned that I may have potentially...looking at the 'Sample
Probe
Profile', the main identifiers that come up (and which I have used in
LIMMA) are 'PROBE_ID' and 'SYMBOL', the first row being ILMN_1762337
and
7A5 re…
updated 12.5 years ago • William D'Avigdor
a time course experiment and was told that with the
design I plan I would not be able to use limma for analysis and need
to use MANOVA. I want to know whether this is true and whether there
is a different experimental...design I can use that would make it
possible for me to use limma. (Simply 'cause I've used limma before ,
but never used MANOVA). Any other comments about the experiment and
exper…
preformatted">
Hi all,
I was wondering how the p-value correction using fdr works.
The following Limma packages command topTable(fit,number=100,
adjust="fdr") corrects the p-values but I dont know which is the
percent of false
I am using an R package to perform an EWAS. The package uses `limma` to fit the model for each CpG site. I check the code for `lmfit`, specifically the function to fit a robust linear model (`mrlm...function uses `rlm` form `MASS` in a for loop over the features (e.g., genes). Is there a way in `limma`, without having to modify the package, to perform this step in paralle? Thank you
Dear all,
I would be very grateful for some desperately needed help.
I am trying to run backgroundCorrect command in R after I loade the limma package. However, I came up with an error code saying: Could not find function "backgroundCorrect"
I am sure that I have...some desperately needed help.
I am trying to run backgroundCorrect command in R after I loade the limma package.&nb…
updated 10.2 years ago • d.leung
div class="preformatted">Dear List,
I am using limma to analyze a affy ST1.0 dataset.
I have 6 patients from which I have two tissue types: tumor and non-
tumor.
One of the sample...the correlation using duplicatedCorrelation
function(please see code below). Therefore, I cannot do limma fit as
usual.
> library(limma)
> target<-read.table("target.txt",header=T,sep="\t"…
div class="preformatted">Dear Helper,
I am interested in using 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
bwss <
<div class="preformatted">Hello,
I'm using limma to normalize and analyse two colour dye swap arrays.
In the output file I am getting two different p values:
I. p.value
II...div class="preformatted">Hello,
I'm using limma to normalize and analyse two colour dye swap arrays.
In the output file I am getting two different p values:
I. p.value
div class="preformatted">I had a few quick questions about the limma models. The first is when
writing these to a file, the fold changes would be the "Coef" column,
not the A column, which is the...the
probe ID, I wanted to see if there was a way to attach the remaining
gene annotation but the limma documentation isn't clear on how to
accomplish that.
Here is how I am currently performing the…
updated 12.8 years ago • Cornish, Joseph NIH/NIAID [F]
divided over 2 chips, give rise to 2 cel files, and use
different
annotation packages.
As I am no limma-veteran, I wondered if there was a way to concatenate
the data from these files before or after reading it into limma as
Hi all,
I am trying to take data from a scanner that is not part of the "core"
group
supported by limma, and create an RGList object from it, using the
minimal
components as defined in the limma docs. I've read in the CSV file
On Behalf Of Maria
Fookes
Sent: 11 March 2004 11:05
To: bioconductor@stat.math.ethz.ch
FAO Limma developers,
I have started to use the limma package for a couple of two-colour
hybridization slides RNA/RNA... can anybody
div class="preformatted">Hi everyone,
I have a question concerning spotted array analysis and limma.
The analysis is working fine except I'm not sure what the out put
means.
I have sample A and samlpe B on an array (3 replicate...slides) and in
limma analysis I put sample A as the reference.
Therefore the results I get, are they the genes up/down regulated due
to sample
<div class="preformatted">Dear Muralidharan V,
See the case study in the limma User's Guide called "Section 11.8.
Agilent
Single-Channel Data: Gene expression in thymus from female Wistar
rats".
The description on GEO says that this is 8x60k data.
As far as I know, there is no difference in the analysis steps for
4x44k
or 8x60k arrays.
Best wishes
Gordon
> Date: Fri, 27 Apr 2012 …
updated 13.7 years ago • Gordon Smyth
<div class="preformatted">Hi BioC,
For 3 experimental groups in LIMMA, when vennDiagram
is generated based on :
mask <- c(1,1,1,2,2,3,3,3);
design <- model.matrix(~ -1+factor(mask));
colnames(design) <- c...div class="preformatted">Hi BioC,
For 3 experimental groups in LIMMA, when vennDiagram
is generated based on :
mask <- c(1,1,1,2,2,3,3,3);
design &…
div class="preformatted">Hi bioconductor group,
I am using the limma package for most of microarray analyses in our
Department
(Genetic). It is extremely useful. I would like to share results
updated 20.7 years ago • gisberto.cicero
and my aim is to analyse microarrays. Now
I'm trying to analyse them with R (1.7.1). I use the limma package and
my data are created with imagene (.txt files). And I'm not able to
make
R understanding what I mean. I know, I have
div class="preformatted">I am using the Limma package 1.6.1 to normalize Imagene files.
Reading the source code I was wondering if there is a particular
reason to
div class="preformatted">Hi,
I am trying to analyze some quantarray files using limma Guide, when
suddenly it gives me the following error at the background
normalization
step (using normexp method and
average
the two technical replicates (there is a function avearrays in the
developmental version of limma for this purpose), or just choose the
technical replicate that looks of highest quality and drop the other
one.
Best wishes...gt; To: <bioconductor at="" stat.math.ethz.ch="">
> Subject: [BioC] unbalanced block design using limma
> Message-ID: <002801cb5c1d$20f9cd4…
that works for the Imagene data
files.
Has anybody dealt with single-channel Imagene data using Limma before,
if so can you point me in the right direction? (I have searched
through the archives, have the Limma manual and a couple
updated 15.1 years ago • Carla Zammit
div class="preformatted">Hello everyone,
I tried to use limma package to read cDNA data into R, I tried the
samples
data
swirl, it all works, but my cDNA data is not the same as the sample...I am wondering is any way I can manupiated the
function to be
able to read customed data format with limma package, like pick up
colume="string", just as read.marrayRaw()?
Any idea is greatly appreciated!…
data to do
hierarchical clustering. But I don?t know how to save the normalized
data from LIMMA.
Below is the code:
library(limma)
setwd("C:/Documents and Settings/JWang/Desktop/analysis with R/RAO")
targets <- readTargets
updated 17.3 years ago • Wang, Jixin
gt;Subject: Re: [BioC] How to do normalization without
backgroundsubtraction
>in limmaGUI or limma?
>Date: Mon, 20 Oct 2003 14:56:34 +1000
>
>At 02:48 PM 20/10/2003, ying chen wrote:
>>Hi guys,
>>
>>I just wonder is there...any option to do normalization in limmaGUI or
limma
>>WITHOUT background subtraction?
&…
updated 22.2 years ago • ying chen
<div class="preformatted">Hello everyone,
First: Im really sorry for posting this because Ive found several
topics
in the mail archive, but I cant seem to get any smarter.
Backgound: I have 6 patients which cells have been divided into two
groups: annexin positive and annexin negative, thus having 12 samples
from 6 patients. In addition the 12 Affymetrix arrays have been
produced
at two d…
Hello,
I just wanted to get a detailed answer on how limma handles missing values.
I am working on proteomics data and already filtered out proteins having many missing values...However, some missing values will remain in the data. I then use limma to fit a linear model and wanted to ask how limma is treating these missing values. From the internet, I cannot find a clear
updated 3.8 years ago • Arend
div class="preformatted">Hi BioC,
I have a question regarding the output of a LIMMA. I have 2 colour
data with a constant reference.
Some googling lead me to some references that as I have a constant
dereference...I can set up a paired comparison as in the limma example.
I have the following targets file
> targets
Filename Cycle State MouseNo
File1 File1 Cycle1 State1 …
<div class="preformatted">Hi,
I am going through the limma User Guide and am having a problem using
contrasts.fit for my data.
I have three biological replicates, two of which have...div class="preformatted">Hi,
I am going through the limma User Guide and am having a problem using
contrasts.fit for my data.
I have three biological replicates, two of which...deprecated in favour of mo…
div class="preformatted">Hi,
I would like to know how to export non log transformed data from limma
after normalization.
Also, I would like to know if any of you have experience with among
slide
normalization for cDNA...microarrays experiment as implemented in limma.
This
seems intuitively important but I would like to know what are the
potential
drawbacks, if any.
Thanks for your help
updated 21.9 years ago • Christian Landry
the
duplicateCorrelation consensus correlation you got from Windows.
Best wishes
Gordon
>[BioC] Limma - error when using duplicateCorrelation - Windows ver.
Linux
>Jakob Hedegaard Jakob.Hedegaard at agrsci.dk
>Tue...Jan 16 15:19:38 CET 2007
>
>Hi List
>
>When using duplicateCorrelation in Limma running
>under Linux I am receiving the follo…
<div class="preformatted">Dear
Is this also the reason why there is a difference in the
(differentially
expressed) gene lists of a-(b+c+d) and venny(a-b,a-c,a-d)?
a-(b+c+d): putting the b, c and d values
in one
group (b+c+d) and using limma
venny(a-b,a-c,a-d): using limma on the separate groups and
create a list by looking at the intersection of de…
appears to be a slightly more complicated situation than the one
proposed in the section 8.7 of the limma users guide (p.45) or by
Jenny
on this post:
https://stat.ethz.ch/pipermail/bioconductor/2006-February/011965.html
In...because they are random "strains"
that happened to end up in phenotype H or L.
Can I design this in limma? Is there a source of information about how
to handle with this?…
div class="preformatted">Hi limma users!
I have two quick questions
1)I know that setting wt.fun=wtflags(0) in read.maimages() exclude
flagged spots from
updated 19.9 years ago • daniela.marconi@libero.it
sort so that I can copy and paste the column gene info from
GPR file into toptable? I don?t want LIMMA to sort out the genes for
me.
Many thanks.
Best Regards,
Wang
</div
class="preformatted">I just installed the latest version of R (2.2.0) and reinstalled and
updated limma. When I ran duplicateCorrelation I got the following
warning (presumably 22500 times).
'randomizedBlockFit' is deprecated
10 arrays, HG_U133A, seperated into
unpaired
two groups of 5 arrays each. I processed the data using LIMMA and
dChip. For
dChip, I used all the default setting. The resulted differential
expressed
genes of the two have only less
div class="preformatted">sltucker at artsci.wustl.edu writes:
> Hi,
>
> I am new to limma and am having problems reading Scanarray Express
.csv
> files into limma via read.maimages. I am running R version 2.4.1...and
> limma version 2.9.17.
>
> I tried...
>
>>RG<-read.maimages(files, source="scanarrayexpress", path=…
13:04 -0400
>From: "James W. MacDonald" <jmacdon at="" med.umich.edu="">
>Subject: Re: [BioC] Limma contrasts questions
>To: Sean Davis <sdavis2 at="" mail.nih.gov="">
>Cc: Bioconductor <bioconductor at="" stat.math.ethz.ch...gt;
>Hi Sean,
>
>Sean Davis wrote:
> > Just ANOTHER limma contrast matrix question:
> &a…
Ken Termiso" <jerk_alert at="" hotmail.com="">
> Subject: [BioC] Exact structure of RGList object (limma)
> To: bioconductor at stat.math.ethz.ch
>
> Hi all,
>
> I am trying to take data from a scanner that is not part of the...core" group
> supported by limma, and create an RGList object from it, using the
minimal
> components as defi…
div class="preformatted">
Hi All
(using R 1.8.0, limma 1.5.1)
I'm slightly confused with the composite normalisation
which I'm guessing you can only use for positive controls...at
Message: 3
Date: Thu, 21 Aug 2003 22:04:19 -0400
From: paul.boutros@utoronto.ca
Subject: [BioC] limma: normalizeWithinArrays using composite method
To: bioconductor@stat.math.ethz.ch
Message-ID: <1061517859…
updated 21.8 years ago • Jason Skelton
think of this as a one-channel analysis). The
usual
ANOVA seems to be at odds with what we get from limma (ignoring the
eBayes
step, which clearly cannot be recovered from the classical treatment).
The usual ANOVA (t treatments...MS(B)/MSE (although we
don't
really care about this)
error=T*B ntb-t-b+1 MSE
However, the Limma manual suggests using duplicateCorrelation and
block to
handle bl…
div class="preformatted">Hi,
Could someone tell me if limma can be used for matched data? If not,
any suggestions? The cases and controls were age, gender and race
matched. I could have
<div class="preformatted">I've read the users guide but I'm not clear whether limma is able to
calculate paired t statistics?
e.g.
Person A, B, C, at time 0, and 1 hour after treatment-- in which I am
interested in...div class="preformatted">I've read the users guide but I'm not clear whether limma is able to
calculate paired t statistics?
e.g.
Person A, B, C, at time 0, and 1 hour a…
disease-
free.
All done on Affy microarrays.
Are there any obvious reasons why one would consider limma over GEE
for
testing for conditional or disease related outcomes?
Cheers,
Michael
[[alternative HTML version deleted
<div class="preformatted">Dear everybody,
I send to you this email because I begin in the analysis of gene
expression and I have some question about the limma package .
In fact, I work on Eucalyptus, and now we have only the expression of
a hundred of gene; we are not at the scale of the...you this email because I begin in the analysis of gene
expression and I have some question about the…
gt; To: bioconductor <bioconductor at="" stat.math.ethz.ch="">
> Subject: [BioC] romer in limma question
>
> Hello list
>
> I'm being a bit stupid with romer (for GSEA) in the limma suite. In
> order to run the analysis
<div class="preformatted">Dear Som,
The usual way to deal with the donor effect is to include a factor for
donor in the design matrix. This ensures that all your comparisons
are
made within donor:
design <- model.matrix(~Donor+Dose*Time)
Usually I would prefer to correct for the batch effect in the design
matrix, rather than pre-correcting with ComBat, because it ensures
that
…
updated 14.7 years ago • Gordon Smyth
on the different methods.
Best wishes
Gordon
Original message:
[BioC] Choosing results from LIMMA analysis
Sharon sharonanandhi at gmail.com
Wed Aug 2 14:32:08 CEST 2006
Hi All,
I have used limma to analyze the time course
updated 19.4 years ago • Gordon Smyth
<div class="preformatted">previously, I have used limma for 2 colour array analysis.
I now have a new data set from Nimblegen arrays in which RMA
normalization has been completed and I wish to identify differentially
expressed genes from the allcalls.txt file which is a table of
expression values for all the treatments in one file
Question:
if I wish to do a single channel analysis in "limm…
div class="preformatted">Dear Adrian,
I assume that you're already read the limma User's Guide advice:
"Print-tip loess is also unreliable for small arrays with less than,
say, 150 spots per print-tip
group...Steward adrian.steward0405 at gmail.com
Mon May 21 19:52:56 CEST 2007
Hi all,
I am using the limma package to analyze a multi-species cDNA array,
2-colour
reference design. The probl…
updated 18.6 years ago • Gordon Smyth
<div class="preformatted">Dear LIMMA users,
Hello. I am analysing single colour microarrays in LIMMA and am facing
some obstacles, which I am not sure have a solution at all. So
wondering
if someone can confirm this or illuminate me on why these errors.
I have a really bad experimental design. It is a simple pair-wise
comparison between mutant and a control conditions. I have 7 samples,
3…
<div class="preformatted">Dear users,
I'm having some troubles in figuring out what's going on in limma.
I've got some expression data from Agilent microRNA platform, I've
pre-processed them, and wanted to do some easy differential expression
analysis. Out of 1368 miRNAs (no filtering performed) there are 758 of
them which show EXACTLY the same value on all of the 24 arrays
involved. Arrays…
across the RNA samples, then the simplest and most
robust approach to di erential exis to use limma-trend. This approach will usually work well if the
ratio of the largest library size to the smallest is not more than...3-fold.
In the limma-trend approach, the counts are converted to logCPM values using edgeR's cpm
function:
> logCPM <- cpm(dge, log=TRUE, prior.count...do…
updated 5.3 years ago • linouhao
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