<div class="preformatted">Dear Bioconductor:
We have a affymetrix time course experiment with repeated measurements
taken at 0 minutes, 30 minutes and 240 minutes following infusion of
insulin. There are 10 arrays for each time point. We used gcrma to
pre-process and normalize our expression data.
We want to use Limma to analyze differential expression in this time
course experiment. W…
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bioinformatics,
computational biology, genomics, data-mining, and related areas.
Call
for papers (Deadline Extended): BCBGC-10, USA, July 2010
The
2010 International Conference on Bioinformatics, Computational
Biology...pools and
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updated 16.0 years ago • John Edward
to perform differential expression analysis on some ATAC data. However, all I have is counts table for peaks (no beds or bams) and a meta table with the sample names and conditions they belong to. Is there a way to use diffbind...any benefit over simply using DESeq2 or edgeR?
Thanks for the help in advance!
#Fake example table
peakname condition1r1 condition1r2 condition2r1 condition2r2
…
updated 6.9 years ago • pgontarz
Because of technical limitations due to library prep time and index diversity, all Type 1 sequencing experiments were prepped and sequenced in one run, whereas Type 2 experiments were divided in 2 unequal batches. It is not possible...design = ~ patient + time) ``releveling for time = 0.
Nevertheless, as I have no sequencing batches in Type 1, I can do this without any problem; it beco…
updated 8.3 years ago • gdagstn
Are there tools implemented in Bioconductor that allow one to use technical replicates to batch correct. Meaning, if one has a group of samples that are repeated across known batches, are there tools that can use these...samples for batch correction
updated 9.6 years ago • Juliet Hannah
gene was down or up regulated
at different time points per breed and I want to have these info in a
table.
To be more specific :
> PL<-read.csv("PietrLand.csv",header=TRUE)
> dim(PL)
[1] 6236 4
> class(PL)
[1] "data.frame"
> PL[1:4,]
Gene.name...1
3 Ssc.14467.2.S1_a_at 1 1 1
4 Ssc.19413.1.A1_at 1 1 1
> q&am…
updated 19.5 years ago • daphne mouzaki RI
Hi,
I am doing RNA-seq analysis using limma and edgeR, I have 48 samples and 2 batches. I built MDS plots (see below), and now my question is do I have a batch effect I need to correct for or not? My understanding...is if batches cluster together on MDS/PCA plot, it's an evidence that batch effects are present, am I right?
<img alt="" src="https://imgur.com
In Bioconductor, it is required that the tarball size should be <= 4MB but my package's tarball size is 50MB. I checked the folders and found that the actual package is less than...1MB. Why is the size of the package's tarball high
updated 8.7 years ago • Mohamad S. Hasan
model could be explained by sex
svafit <- sva(geneExpression,mod) # we suspect some batch effect but we don't know from which variable it comes, so we use sva
svaX<-model.matrix(~sex+svafit$sv) # we adjust with the...df.residual[1])
Code2
library(limma)
mod <- model.matrix(~sex+batch) # we explain our model with sex and some b…
updated 3.1 years ago • Lenny186
div class="preformatted">For normalization the batches of slides do not matter if you use the
usual
2-color normalization methods, which normalize each slide separately...If
you want to do multi-array normalization, you need to read all the
arrays
into a single batch.
However, for analysis, you likely want to use some type of ANOVA. For
this, it is more convenient to read in all of the arra…
updated 22.1 years ago • Naomi Altman
I understood the examples of the Omixer pacakge. Because when I try to use a layout for multiple batch I was not able to make it work.
Now that I made sure there are enough sites to allocate all the samples it tells me that the...with `filter()` input `..1`.
#> ℹ Input `..1` is `mask == 0`.
#> x Input `..1` must be of size 288 or 1, not size 237.
Omixer_index <- omixerRand(s…
updated 4.7 years ago • Lluís Revilla Sancho
Look for reference about paired analysis about microarray.
I have a data set about a microarray experiment for same patients
before and
after treatment. Data Layout is show in belwo
Table 1
Patient 1 Before surgery Patient...of interest, classify patients, and identify
patients who respond to the surgery. Also, the sample size needed for
further experiment is of interest. Typical …
updated 21.9 years ago • Haiyan Wu
div class="preformatted">Dear friend,
I'm trying to use your ComBat R script to eliminate batch effect when
combine high-throughput gene expression data from different batches.
However, there is an issue about the...skip=1,'clinicaldata.txt')
Reading Sample Information File
Reading Expression Data File
Found 3 batches
Found 66 covariate(s)
Error in `[<-`(`*tmp*`, , i, value = c(NA, NA,…
updated 11.5 years ago • Shaowei Wu
gene 2 in lines 51-98.
<span style="line-height:1.6">My question is whether or not there is a batch correction function based on means or medians which I can apply prior to the various normalization functions in the...package, and what that would be called. For instance if one batch of 24 samples routinely has high Ct values compared to other batches I would like to adjust the Cp…
Hi all,
First post here, so apologies if I haven't explained anything clearly/followed standard guidelines.
I'd like to create a summarized experiment object for downstream analysis of my count data from RNA seq analysis. The way I do this is something like this...I haven't explained anything clearly/followed standard guidelines.
I'd like to create a summarized experiment object for …
updated 8.8 years ago • krc3004
div class="preformatted">Dear all,
I would like to use Combat to correct for different batches
(extraction date, hybridazation and amplification). In the description
there is only on variable for batch, but i can...set more then one
covariant, so should I use one for batch and the rest as covariants?
Thanks you very much</div
updated 13.3 years ago • cirruswolke9@googlemail.com
thead>
<tbody>
<tr>
<td>
<table border="0" cellspacing="0">
<tbody>
<tr>
<td>17-0117</td>
</tr>
</tbody>
</table>
</td>
<td>
<p>NR_Co</p>
</td>
<td>T0</td>
<td>T0_NR_Co</td>
</tr>
<tr>
<td>
<table border...0" cellspacing="0">
<tbody>
<tr>
&…
updated 7.4 years ago • mat.lesche
Hi,
I want to use edgeR for DEGs between two groups, but I find two batches in samples. So I intend to use Combat to adjust for differences between batches. I know edgeR is designed to
updated 11.0 years ago • zhouxiuqing
Hi all,
I wanted to know if it is possible to remove 3 batches using "limma".
I have sequencing data with three possible batch effects: age, gender and working sets.
As far as I understand...using limma's "removeBatchEffect" enables to remove only two batches categories by defining "batch" and "batch2"
removeBatchEffect(x, batch=NULL, batch2=NULL, covariates=NULL,
…
updated 6.1 years ago • Matan G.
Hello! I am following the ___Aaron T Lun et al. 2016___ paper to analyze my brain scRNA-seq data, but I am blocked in the step of gene filtering. I have my data in an _sce object_ and I...Hello! I am following the ___Aaron T Lun et al. 2016___ paper to analyze my brain scRNA-seq data, but I am blocked in the step of gene filtering. I have my data in an _sce object_ and I have...ave.counts >…
updated 8.0 years ago • Marina V.V.
genome="hg38", tablename="refGene")_
_-----_
I am able to download the refGene table, but then receive the following error:
_-----_
_Download the refGene table . . . OK_
_Download the refLink table . . . Error in normArgTable...value, x) : unknown table name 'refLink'_
_-----_
Upon looking on the hg38 genome browser it appears that the refLink table is still connected to the...refGene tabl…
updated 9.5 years ago • cmarcone
I am performing a differential expression analysis between treated and untreated cell lines using DESeq2. The samples were sequenced in two different batches, however, there is a perfect confounding of the conditions and the batches. All controlled samples are in one batch and all treated samples are in the second one. The perfect confounding does not allow to remove batches or even account for t…
updated 4.9 years ago • rina
I have RNA-Seq data from two batches and know there is significant batch effect in the data.And I just want to get the normalized data without batch effect...row.names = FALSE)
> ddsHTSeq1<- DESeqDataSetFromMatrix(counts.spikein, colData, design =~batch+condition)
> dds1<-DESeq(ddsHTSeq1,full=~ batch + condition, reduced=~batch, test="LRT")
estimating size factors
…
updated 6.9 years ago • Nicola
variables is affecting my results.
For example, I am wondering if it makes sense to include "batch" in my design. Before doing any analysis, I made PCA plots from my data, and the samples do not seem to cluster by batch. If I...run DESeq to compare across disease state without controlling for batch in my design and then generate a heatmap with hierarchical clustering, the samples from the sam…
updated 5.0 years ago • lransom
Can I use ComBatSeq function instead of ComBat to adjust for batch effect in microarray data?
I know the description of ComBatSeq is for RNAseq but when I tried both functions, ComBatSeq...was more efficient in removing batch effect compared to ComBat.
![ComBat-Seq][1]
![ComBat][2]
[1]: /media/images/40a00310-c2ca-424d-9268-fc58f939
[2]: /media/images/9bb0aca6
updated 10 months ago • Shaimaa Gamal
Hi, after an RNASeq analysis using Limma I obtained a table full of genes by using the topTable() function. So I have a csv, comma separated, formed by GENEID(ensemble), ENTREZID, SYMBOL...there a way to search the most significant genes associated to a specific disease mentioned in some papers? Because for e.g. the top 5 genes are not mentioned in any paper to be related to some diseases. The ta…
updated 5.2 years ago • Will
Hello,
I have a time course RNAseq experiment with 2 different genotypes and 2 times (0h and 2h), there are 3 replicates each time
I am looking for a way to output...2h VS 0h in condition B). I don't know if it is right to directly compare the FoldChange from both tables. Also, some genes do not have the same expression level at 0h.
I was more thinking of making a new analysis using a desi…
updated 3.1 years ago • Julie
and there are two sequencing platforms used, illuminaHiseq and IlluminaGA. Is there a way to remove batch effects in DESeq2 package prior to differential expression or does the GLM remove it automatically (which i dont hink
differential gene expression between healthy and KO mice. I know that there is a very strong batch effect that I have to adjust for. I read both on this forum and on _Biostar_ that it is generally recommended to include...the batch effect in the limma model instead of using for example _Combat_seq_ to adjust for the batch effect.
I wanted to make sure...that limma can appropriately control for…
updated 4.0 years ago • nhaus
div class="preformatted">
How do I generate a simple table similar to the following link in R
http://www.fedstats.gov/policy/publications/wp1fig1_text.html
Table 1 Poverty
updated 15.8 years ago • David Lyon
class="preformatted">Dear list,
I got 12 Affymetrix arrays for 4 RNA samples, 3 replicates(from 3
batches individually) for each sample. I want to look at the
differential expression between these samples. While after clustering...we found obvious batch effect within the data, so we decided to add
the batch effect into the linear model. I set up the design matrix as
followings...is any proble…
updated 16.5 years ago • Yuan Hao
div class="preformatted">Dear All,
Is there an equivalent of the table function for a GenomicRanges
object?
Best,
Vedran
--
Vedran Franke
Bioinformatics Group,
Department of Molecular Biology
updated 13.3 years ago • Vedran Franke
Hi bioC community,
Until now I used comBat to remove the batch effects present on my datasets.
After reading the article "Methods that remove batch effects while retaining group...content/early/2015/08/31/biostatistics.kxv027.full.pdf>, I decided to block for batch effect in limma in the case where the groups are distributed between the batches in an unbalanced manner.
But I am wondering...…
updated 10.4 years ago • eleonoregravier
As far as I understand, The process by which DESeq2 models a batch effect is close to :
Subtracting the arithmetic mean of the batches' expression values from the genes, on a per-gene basis...Is it possible in DESeq2 instead of modelling only an additive batch effect, to model a multiplicative one as well? For example, divide the expression levels per gene by the batch-specific...differential ex…
updated 6.4 years ago • Sam
Hi all,
I have a problem in figuring out how to include the batch effects in the design formula of DESeq.
In particular I have to test the effect of one condition (Low protein diet vs Control...liver samples (24 for each condition). The problem is that I sequenced the samples in two separate batches (always keeping Treated vs Control in each batch) and different sequencer.
So I have 2 big …
updated 3.4 years ago • Flavio
the same gene universe for 2 different gene enriched sets, there are different number of GO term sizes for the same GO term:
An example
Gene set enr: 1480
<table border="1">
<tbody>
<tr>
<th>GOBPID</th>
<th>Pvalue</th>
<th>OddsRatio</th>
<th...ExpCount</th>
<th>Count</th>
<th>Size</th>
<th>…
updated 9.0 years ago • tlaguna
Hi, I am new to batch effect correction and apologize if this is a naive question.
My goal is to determine how similar my cell line is to the...database. I have the RNA-seq profiles for both samples, but they are obviously from two different batches, and any possible biological differences are confounded with batch.
A colleague of mine suggested that I can still...batch effect correct to check …
updated 12 months ago • bbao
Dear Users,
We have a CyTOF experiment containing 91 samples distributed in 10 batches, with one anchor for normalization in each of these batches.
However...Dear Users,
We have a CyTOF experiment containing 91 samples distributed in 10 batches, with one anchor for normalization in each of these batches.
However, I can't figure out how to make it work:
I would like to tell the fu…
updated 6.9 years ago • Florent
Hi,
I have a question concerning insertion size when using MEDIPS.
When setting paired = TRUE in MEDIPS, you will get a mean insertion size as well as standard deviation...Mean insertion size: 204.4319 nt
SD of the insertion size: 57.93392 nt
Max insertion size: 602 nt
Min insertion size: 49 nt
Does the insertion...size include the reads or is it the number of nucleotides be…
updated 9.2 years ago • stb
ALL,
in conjuction with one previous post about the correct implementation of ComBat() function for batch effect correction, \[<span style="line-height:1.6">__https://support.bioconductor.org/p/77726/__\]</span>
i would like to ask...dl=0__
So, i understand that the black line represents the kernel estimate of the empirical batch effect density, and the red the parametric…
updated 10.1 years ago • svlachavas
div class="preformatted">What anova table do you want exactly? lmFit() fits a linear model for
each probe. Do you want
55,000 anova tables if there are 55,000 probes? That...34:15 -0500
> From: Jianping Jin <jjin at="" email.unc.edu="">
> Subject: [BioC] limma anova table?
> To: BioConductor_list <bioconductor at="" stat.math.ethz.ch="">
> Message-ID:…
in itself a simple form of spatial
normalization (as well as intensity-based normalization). In my
experience,
print-tip-loess does most of what spatial normalization would have
done.
But, as you say, if you really do want to...formal 2D normalization
you'll
have to do it outside of limma.
>I am also running a Genechip experiment, with four time points and
three
>treatments (A,B an…
updated 22.5 years ago • Gordon Smyth
Hi,
I would like to use _sva _package to adjust for the effects of batch on two independent datasets. Ideally, one dataset should be the training set, while the second one is for prediction. My...Hi,
I would like to use _sva _package to adjust for the effects of batch on two independent datasets. Ideally, one dataset should be the training set, while the second one is for prediction. My underst…
updated 10.5 years ago • Farshad Farshidfar
Hello, usually I load the condition table from a table in order to have a data frame with a column called condition that I put in the design formula:
<pre>
dds = DESeqDataSetFromTximport
updated 8.8 years ago • ribioinfo
keeping into account only the stage when creating the DE object like this (an example of my design table is at the end of the post):
<pre>
(design=~stage)</pre>
Using this approach and following the guidelines described in the tutorial...Another alternate approach I thought was to use sva or other packages to remove the "timepoints batch effect" in each stage, however I still haven…
updated 9.0 years ago • wariobrega
something extremely stupid here.
I have 76 plates(in 96 well format) in dulipate, and first 3 batch
each
has 20 plates within a batch(with duplicate, which means 40 plates
total
for each batch). my code to define the batch...to
the
description of the package I need to define a array with dimension of
(96*76,2,1) to feed to "batch" function)
"DL" is my cellHTS object;
ind=c(rep(1:3,each=96*20),…
a user visible change to the empirical Bayes procedure used in
the
limma package. I have changed the hyperparameter estimation to make it
less
sensitive to sample standard deviations which are zero to machine
precision...The only exception is for data sets which have many
exactly zero standard deviations, which may experience somewhat less
smoothing than at present.
The data sets for which the c…
differential transcript level expression analysis and I have 3 groups that were sequenced in 5 batches
I am trying to run swish on the data to get differentially expressed transcripts however my batch distribution is...8 8 1
> Batch4 0 11 12
> Batch5 8 8 8
As some batches are 0 or 1 when I run the following command between two groups I g…
updated 2.6 years ago • priyanka
if anyone knew where the python module is to carry out pathway analysis using the methods in the paper by Kim and Volsky (2005) in their paper "PAGE: Parametric Analysis of Gene Set Enrichment paper"? It is not clear if they...produced a python module from the paper and if they did i have not been able to find it!
Any help would be great to point me in the right direction
Thanks
Danie…
updated 9.0 years ago • danielle.newby
<div class="preformatted">2009 World Congress on Computer Science and Information Engineering
(CSIE 2009)
March 31 - April 2, 2009
Los Angeles/Anaheim, USA
http://world-research-institutes.org/conferences/CSIE/2009
CALL FOR PAPERS, INVITED SESSIONS & EXPO
The Los Angeles/Anaheim area is known for its many renowned
attractions, such as Disneyland, Universal Studios and the
Hollyw…
updated 17.5 years ago • Hongping Wu
to find differentially methylated CpG sites. Both of the datasets are from EPIC array, but different batch(batch 0 and batch 1).
I've already tried to correct the batch effect using [Harman batch correction][1]
```r
shifted_betas <...cex.main=0.7)
shifted_ms
methHarman <- harman(shifted_ms, expt=targets_pr$Sample_Group,
batch=targets_pr$batch, limit=…
updated 2.2 years ago • kyj2226
So, I've had the BHC package working for a time course experiment before. I'm trying to use the multinomial option instead of the timecourse one and it's breaking, spectacularly...So, I've had the BHC package working for a time course experiment before. I'm trying to use the multinomial option instead of the timecourse one and it's breaking, spectacularly. The basic use case in the documentation …
updated 10.9 years ago • b.curran
Hello,
I'm struggling with batch correction for RNA-seq data in DESeq2.
For example, my colData looks like this (10 samples, 6 controls+4 treatment, belong...to 2 batches):
samples condition batch
100 PH7 1
101 PH7 1
103 PH7 1
63 PH7 1
64 ctr 1
74 ctr 1
…
updated 6.6 years ago • Rimma
Dear all,
I am working with a RNASeq data from an Arabidopsis experiment. The plants have been subjected to nitric oxide treatment for 3 hours and for 8 hours. I would like to find differentialy...the section "3.3.3 Treatment effects over all times" of edgeR user guide.
The design of the experiment is 3 biological replicates for each of the 3 samples:
<table border="1" cellpadding="1" cells…
Hi:
I am experimenting preprocessed Affymetrix microarrays expression data matrix (Affymetrix probe-sets in rows (32830 probesets...in columns (735 samples)) for my downstream analysis. However, I have `pheno` metadata for the experiment observations.
**data that I used**:
> dim(eset_HTA20)
[1] 32830 735
> eset_HTA20[1:3, 1:3]
Tarca_001_P1A01 Tar…
updated 6.7 years ago • Jurat Shahidin
packages*
What should I do to load the airway package
sessionInfo( )
*R version 4.1.2 (2021-11-01)
Platform: x86_64-apple-darwin17.0 (64-bit)
Running under: macOS Monterey 12.1
Matrix products: default
LAPACK: /Library
updated 4.1 years ago • j.jacob1
to provide biological software support as needed.
Other duties as assigned.
Teaching and Training: (10%)
Prepare and deliver training materials for high performance, high throughput biological computing to NCSA...CS, ECE or related field. Alternative degree fields will be considered if accompanied by equivalent experience as it relates to current NCSA projects.
1-3 years of experience…
updated 4.2 years ago • Jenny Drnevich
colnames(pData(eset_NONE));
table(pData(eset_NONE)[,"**Study**"]);
table(pData(eset_NONE)[,"**Disease**"…
updated 6.9 years ago • pratikshasharma47
Hi
I am almost finished my package and the paper is nearly done too. Which order do I submit these in? Do I wait for it to be accepted by the bioconductor then submit to journal
updated 8.8 years ago • chris86
very well if your log-data are fairly normally distributed
(within each gene) and if your sample size is relatively large (say
~15-30). If you have a small sample size or if your data (within each
gene) are not normally distributed...gt; Content-Type: text/plain; charset="iso-8859-1"
>
> I'm trying to analyze an RNA-seq experiment where the PCA plot shows
better
> clustering …
updated 12.7 years ago • W. Evan Johnson
Recent ...
Replies
Comment: tximeta cannot open annotation gtf?
by
Michael Love
43k
Yes, so this is the same type of error you would get if you tried to assemble a *SummarizedExperiment* manually with tximport + GTF process…
Answer: tximeta cannot open annotation gtf?
by
ATpoint
★
5.0k
> Timeout of 60 seconds was reached
You have to increase the default timeout limits for downloads, `options(timeout=3600)`. GENCODE serve…
Answer: GSEA error
by
James W. MacDonald
68k
At a very high level, the way non-model organisms are annotated is by using blast to find orthologs in other species that are well annotate…
Comment: Unable to find ENTREZ IDs
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Adithi
•
0
Hi James,
Thank you so much for your reply. My main goal is to find ortholog genes from chinese hamster gene symbols to mouse gene symbols…
Comment: Unable to find ENTREZ IDs
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Adithi
•
0
Hi James,
Thank you so much for your reply. My main goal is to find ortholog genes from chinese hamster gene symbols to mouse gene symbols…
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