<div class="preformatted">
Hi,
I'd like to use a GLM in edgeR to adjust for a batch effect, though
only one of my four batches has samples from both groups in the
comparisons that I'd like to conduct (pos-nc & neg-nc):
1 2 3 4
pos 3 5 9 0
neg 5 4 7 0
nc 0 0 5 8
I suspect that using a GLM in edgeR to adjust for batch will only work
properly if there's repr…
Order by: Relevance
<div class="preformatted">Hi,
I have an excel file containing Gene name, Regulation, Breed and Time.
I
have two breeds that I
Have symbolised 1=Pietrain and 2=landrace and I also symbolised 7 time
points, 1,2,3,4,5,6,7 for
2,4,8,12,16,24,30 hours that the samples were taken. My problem is
that
I want to create a table
with Time min, Time max for each gene per Breed and I can't think of a
w…
updated 19.2 years ago • daphne mouzaki RI
support vector machine. The data comprises of healthy and disease states which sequenced in 13 batches. I have 2 questions:
1) I used design = ~ batch + condition and when I ran resultsNames(dds), I found that the result is only between...each batch against the first batch whereas I'm looking for all differential expressed genes between healthy and ...find all …
updated 7.2 years ago • Maryam
data looks like as in the PCA plot below - 4 biological replicates of 4 conditions, and there are 4 batches with each batch consisting of 1 sample from each condition. In essence the variation between biological replicates...is larger than the variation in the tested conditions most likely due to batch effects. Likely the wet-lab has processed each replicate of all conditions at different days.
…
updated 2.6 years ago • gtechbio
what would be the best approach to perform clustering on a subset of cells pulled out from a MNN-batch-corrected object.
I used fastMNN from SeuratWrappers to perform a MNN batch-correction and perform an integrated analysis...a cluster of cells and wanted to perform re-clustering.
Should I perform another round of MNN batch-correction on the subsetted object or proceed with the usual analytica…
Biologist/Bioinformatician(x3)__ with an in-depth understanding of biological data and advanced experience in statistics, big data analysis (including machine learning), or other similar fields.
__Responsibilities...biology, computer science and bioinformatics (Profile 1,2,3)
__Qualifications & Experience __
__Profile 1: __
*
…
updated 8.1 years ago • bulfin.triona
cell type. As a simplified example, suppose for a particular gene we have these expression levels:
<table border="1" cellpadding="1" cellspacing="1" style="width:500px">
<thead>
<tr>
<th scope="col">celltype</th>
<th scope="col">human</th>
<th scope...tr>
<td>K</td>
<td>180</td>
<td>360</td>
</tr>
<tr>…
updated 7.0 years ago • mjldehoon
of this Center could work on broad areas of bioinformatics and gain valuable experiences. The members of this Center also have the opportunities to publish high profile papers with prominent authorship...of relevant post-degree work experience is required with a PhD
Lead Bioinformatics Analyst
Six (6) years of relevant experience is required.
Four (4) years...of relevant experience may be acc…
updated 3.5 years ago • xubeisi
and that they belong to extbatch 7._
Most of the samples from batch 7 and even batch 8 had lower RNA yield than other samples.
<img alt="" src="https://i.imgur.com/W4uZzkO.jpg" style="height...are individual samples. Y-axis are counts forced to limits -100K and 100K. Colours denote extraction batches. Red is the offending batch 7 with mostly bad samples. See appearance of negative …
updated 8.2 years ago • rmf
I'm plotting the output of enrichGO from the clusterProfiler package. The font size is so small it is illegible (even in the Vignette here: https://bioconductor.org/packages/release/bioc/vignettes...I'm plotting the output of enrichGO from the clusterProfiler package. The font size is so small it is illegible (even in the Vignette here: https:…
updated 7.7 years ago • stephen.williams
vsd <- varianceStabilizingTransformation(dds, blind = FALSE)
Although I tried to include the batch (Institution) in the design argument, I still see batches in my PCA plot. [This section][1] of the vignette described a solution...I have pasted below:
mat <- assay(vsd)
mat <- limma::removeBatchEffect(mat, vsd$batch)
assay(vsd) <- mat
plotPCA(vsd…
I'm trying to adjust batch effect using `deseq2 limma::removeBatchEffect` like below:
```r
###### Batch Correction with limma removeBatchEffect #######
dds <- DESeqDataSetFromMatrix...design = ~ Samplebatch + cond)
dds <- DESeq(dds)
dds
dds$batch <- as.numeric(dds$Samplebatch)
dds$cond
dds$batch
## vst after adding batch information
vsd_abc <- vst(…
updated 2.7 years ago • vk
Biotechnology Center at the University of Illinois Urbana-Champaign. We are hiring a new analyst and experience in any area of ‘omics data is fine. We will also consider those with lesser experience but the ability to learn on...the job through in-house training. See the full job posting and application site at https://illinois.csod.com/ux/ats/careersite/1/home/requisition
updated 3.0 years ago • Jenny Drnevich
<div class="preformatted">Dear list,
has anyone experience with the package "superpc" for developing a gene
expression based predictor
for survival?
We have (Affymetrix) arrays...div class="preformatted">Dear list,
has anyone experience with the package "superpc" for developing a gene
expression based predictor
for survival?
We have (Affymetrix...and which
consequently have different…
updated 18.8 years ago • Manuela Hummel
p/26983/
Dear John,
You can't expect to be able to estimate more things than your experiment contains information about. In this case, your batches are entirely confounded with patients+treatment...paired samples before and after treatment, and I would also like to take
> into account batch effect.
>
> I am having probl…
updated 10.5 years ago • Gordon Smyth
I am using Rsamtools to scan a BAM file generated with Bowtie2 (local alignment mode). I am interested in the insert sizes. Most of the time, everything works as expected. However, I noticed an issue with soft-clipped reads. If the fragment is smaller...to scan a BAM file generated with Bowtie2 (local alignment mode). I am interested in the insert sizes. Most of the time, everything works as expe…
and Phenotypic data, I run into problems when dealing with Methylation betas due to the presence of batch effects.
To consider:
**1)** Data arrived already normalized using functional normalization (*meffil* package) and batch corrected...I don't have access to the raw data.
**2)** They state (and I confirm using a simple ANOVA) that batch effects are still present even after correction.…
updated 6.0 years ago • lucasmiranda42
well as in the heatmaps of the genes with the highest variability, I am quite sure that there is a batch effect based on the date the samples were processed. This I would like to correct by adding the date factor to the design...whether or not the date is indeed a problem I have plotted the PCA before and after removing the batch effects. The top plot is before, the bottom plot is after removing …
updated 8.2 years ago • Assa Yeroslaviz
<div class="preformatted">Hello all,
I do need some help on analyzing such unorganized data. Please help me
out. Thank you so much!
I basically followed the analysis of multi-level experiments in limma
user guide. But I do not feel right about the code below. Please give
me some suggestions.
# I want to compare Normal vs. Tumor negative, and Normal vs Tumor
positive. There are partial pa…
updated 11.4 years ago • Rao,Xiayu
age2, batch2
age2, batch2
age2, batch2
age2, batch2
Is there a way to normalize the impact of batch on these samples, before I do a differential expression analysis
updated 6.4 years ago • KRA
<div class="preformatted">
Hi Alex,
Here are some references:
WJ Gauderman (2002), "Sample size requirements for matched
case-control studies of gene-environment interaction", Stat Med
21:35-50.
WJ Gauderman (2002), "Sample...div class="preformatted">
Hi Alex,
Here are some references:
WJ Gauderman (2002), "Sample size requirements for matched
case-control studies of gene-environment i…
updated 17.9 years ago • pingzhao Hu
Dear all,
I have the following problem: I have my model (controlling for Batch, Age, Sex) and I am interested in the condition.
dds <- DESeqDataSetFromMatrix(countData = cts,
colData = colData,
design...BATCH + AGE + SEX + CONDITION
Now I need to do some grouping the condition, following vignette with
…
updated 4.6 years ago • Bine
Hi
I would like to correct batch effect using deseq2, to analyze one hundred of RNA-Seq of tumors, without experimental design. 80 tumors were sequenced...in 2018, and 20 in 2019; I can see a strong batch effect whent I plot PCA on reads count or on data after DESeq between 2018 and 2019 tumors.
Usualy I used:
coldata <- as.data.frame...dds<-DESeqDataSetFromMatrix(COUNT…
updated 6.4 years ago • mdidish
I have thousands of samples from `TCGA` retrieved using `TCGABiolinks`. I want to remove the `batch effect` from the datasets. It's mentioned that batch can be detected from sample ID itself
How do we identify the batch...I have looked at [this link][1] get information on `sample ID`, but not specifically mentioned about batches.
Is it a combination of `PlateId`, `ShipDate`, and `Tissue Sou…
updated 2.8 years ago • snijesh
in cell populations of grt vs dgrt using the batch, patients (ind) and condition. But I encounter error as shown below.
<pre>
colData
batch condition ind
u.132p1 u grt b...pre>
dds <- DESeqDataSetFromMatrix(countData = data.grt.dgrt,colData = colData,design = ~ batch + condition)
dds
ddds <- DESeq(dds)
res <- results(ddds)
res…
gt; modcombat = model.matrix(~1, data=pheno) combat_edata1 =
> ComBat(dat=edata, batch=batch1, mod=modcombat, par.prior=TRUE,
> prior.plots=FALSE) combat_edata2 = ComBat(dat=combat_edata1,
> batch=batch2...mod=modcombat, par.prior=TRUE, prior.plots=FALSE)
Or should I set my model matrix with the second batch, while combat-adjusting for first batch, then set …
updated 5.6 years ago • Zach Roe
future samples. I'm using UPC function in the SCAN.UPC package. I saw there's an option to provide batch information for each sample and the batch effect will be corrected. I read the following in the SCAN.UPC documentation...are invoked without batch information; in this scenario, no SCAN normalization will occur."
I have some questions regarding the batch effect:
1. Is...build models on each …
updated 7.3 years ago • y.li.1
Hi,
If there a way to produce **uniformly** **sized** gene models regardless of the number of transcripts? I have attached examples of a gene with two transcripts and another...autoplot(ensdb, GeneIdFilter("MyENSG")) #, names.expr = "gene_id")
R version 4.1.1 (2021-08-10)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 18.04.5 LTS
Matrix products: default
BLAS: /usr/li…
updated 3.9 years ago • rbenel
contaminated lot. I understand that this grouping can be because of either the rRNA contamination or batch effect but I think it is more likely to be because of a batch effect as I don't see exactly the same pattern when I plotted...it with the "old" contaminated samples. When I control for batch effect in my design __(dds< DESeqDataSetFromMatrix(countData, colData, formula(~ batch +&n…
CNR Napoli
The scientific programs of CIBB 2015 will include Keynote Speakers, contributed papers, tutorial and special sessions. The contributed papers will be presented in plenary oral sessions, special sessions...Session Proposal: April 3, 2015
Paper submission deadline: &…
updated 10.8 years ago • rancoita.paola
Hi,
we have RNAseq data with some evident batch effect. We wont to correct this to have batch effect corrected counts to be then used in DESeq.
The idea is to have all the...PCA, hierarchical clustering, GSEA) that use DESeq normalized counts already compenseted for the batch effect.
Is this possible? What is the best tool to remove batch effect on raw counts to obtain data to be then used in …
updated 2.9 years ago • luca.s
Is it possible to generate the html QC tables with a call to ChIPQCreport(), that does not include the commentary and interpretation narrative?
thanks
Ashley
updated 9.6 years ago • ashley.doane
matrices for gene expression designs". I am having some difficulties figuring out how to correct batch effects in my dataset. I tried adding a separate column to the grouping file as follows; and tried to use the following...group <- factor(paste(targets$Treatment, targets$Time, sep = "."))
cbind(targets,group=group)
Batch <- factor(paste(targets$Batch, sep = ","))
#M…
updated 3.6 years ago • venura
well even though I am using the same reference genome and annotation. How would I correct for this batch effect? I have tried RUVSeq's upper quartile normalization but it does not do anything, I have not tried using "negative...or housekeeping genes.
I also have single and paired end data, how do I correct for the batch effects between the two? Thank you
updated 8.1 years ago • llo
Dear Swish/Fishpond team,
I quantified transcripts from a crop plant using Salmon and inferential replicates. Then I wanted to use swish to detect differentially expressed genes across conditions in a pairwise manner.
Using multidimensional scaling, I found a substantial batch effect among biological replicates. So I intended to use the “covariate” argument in swish but an error was returned …
div class="preformatted">Dear all,
We have performed a time-series experiment (2h, 6h, 10h, 48h,
) on
dual-channel arrays where we want to compare gene expression between
treated
and time-matched...design) to use randomized
blocks in
LIMMA to estimate variability between the three microarray batches
(time-courses)?
If affirmative, the R code I would use looks as follows:
> design = c…
updated 18.4 years ago • Serge Eifes
Building most specific GOs .....
Error in result_create(conn@ptr, statement) : no such table: go_bp
```
The problem is due to the fact that I am using a custom OrgDb which doesn't have the `go_bp` table. A custom OrgDb for...a non-model organism that I made using `AnnotationForge::makeOrgPackageFromNCBI()` has these tables:
`tbls: accessions, alias, entrez_genes, gene_info, genes, go, go…
updated 6.8 years ago • psutton
in DESeq2.
In the manual it says that "Normalization factors should include library size normalization".
Does that mean that I should divide each column of the normalization matrix by the
corresponding...sizeFactor, or it will be done automatically?
Additionally, should I use the size of the feature for normalization, or it's inverse:
i.e. if I want to compare reads that fall withi…
updated 9.3 years ago • vedran.franke
S7
14 sample14 2 B S7
15 sample15 2 A S8
```
In this example, batch == 1 has 5 subjects with both conditions per subject, while batch == 2 has 3 subjects, one of which has only one condition. I simplified...dds = DESeqDataSetFromMatrix(countData = counts.mat, colData = sample.summary.balanced, design = ~ batch + subject + condition)
dds <- DESeq(dds)
Err…
updated 4.7 years ago • demisa
class="preformatted">Dear *Bioconductor* users,
Is there some package besides ComBat to deal with batch effects?
YiSong
--
//--------------------------------------------------------------------
-------------------
// We have a hunger of the mind which asks for knowledge
// of all around us, and the more we gain, the more is
// our
updated 15.6 years ago • Yisong Zhen
Hello everyone. I have a question regarding how to interpret the value of the Fold Changes when a batch effect is present.
I am running DEseq2 including the batch in the design matrix, as recommended. When looking at the log2FC...Hello everyone. I have a question regarding how to interpret the value of the Fold Changes when a batch effect is present.
I am running DEseq2 including the batch in…
updated 3.2 years ago • eve.olszanowski
Hello
I am having trouble choosing a model matrix to analyze certain RNA-Seq data set. I will first describe the experiment and afterwards show between which designs I am doubting.
**Design of the experiment**
There are six distinct animals and each animal received the control (untrt) and the treatment (trt). The control and the treatment were separated by a fixed amount of time. This…
updated 5.8 years ago • tmms
I want to make a clustered heat map for the differentially expressed genes I identified with EdgeR where the batch effect was modeled as an experimental factor. To do this, I used the limma package removeBatchEffect() after TMM-normalization...make a clustered heat map for the differentially expressed genes I identified with EdgeR where the batch effect was modeled as an experimental fac…
updated 9.8 years ago • Ekarl2
mso-spl-e:yes;}
span.GramE
{mso-style-name:"";
mso-gram-e:yes;}
@page Section1
{size:8.5in 11.0in;
margin:1.0in 1.25in 1.0in 1.25in;
mso-header-margin:.5in;
mso-footer-margin:.5in;
mso-paper-source:0;}
div.Section1...if gte mso 10]>
<style>
/* Style Definitions */=20
table.MsoNormalTable
{mso-style-name:"Table Normal";
…
updated 23.6 years ago • Niklas Nordquist
1)
#with the example
set.seed(120)
x <- matrix(rnorm(1000*20),ncol=20)
y <- sample(c(1:4),size=20,replace=TRUE)
mydata <- list(x=x,y=factor(y))
train = pamr.train(mydata)
pamr.listgenes(train,mydata,1)
Thanks for help
Alice
nbsp; 30 150</span></code>
<code><span style="background-color:transparent">table(batch)</span></code>
<code><span style="background-color:transparent">batch</span></code>
<code><span style="background-color:transparent...code>
<code><span style="background-color…
updated 8.6 years ago • svlachavas
I have 9 samples now, however when I merge them together to analysis, I can find a obviously batch effect drived by each samples. Especially, T cells are clustered by each sample rather than cell types . So I want to employ...mnnCorrect function in scran package to remove batch and make cells are clustered by celltype rather than sample.
- Before use mnnCorrect, I have some questions . My…
updated 6.6 years ago • xingxd16
at="" mcri.edu.au="">
> Subject: [BioC] Two colour arrays - advice on unconnected design,
> batch effect
> To: <bioconductor at="" stat.math.ethz.ch="">
>
>
> Dear All,
>
> I have limited experience with analysis of two...fit2, coef=2, adjust="BH")
>
>
> Is it sensible to make a coefficent for each of the …
updated 16.1 years ago • Gordon Smyth
<div class="preformatted">
Hello,
I am trying to write a script that will enter miRNA and get the
predicted target genes for that miRNA. I am trying to use various
software to do this, one of them is TargetScan. The problem is that I
don't know how to parse the HTML output table so that I can get the
target genes only.
For example I am search for target genes for the miRNA mmu-miR-1 as
f…
following experimental design, with three biological replicates per `Sample.Type` performed in two batches (two different experimental dates, `Exp.Date`):
> metadata
Sample.ID Sample.Type Exp.Date
1 Ctrl_1 Ctrl 1
2 Ctrl_2...analysis using edgeR, I thought it would be best to use `model.matrix(~Batch + Treatment)` for the model formula, where…
updated 5.4 years ago • rebecca.lea.johnston
Hi all,
I really need help for a problem I have come across since I received another batch of RNA-seq data which I have combined with the first batch. Within both batches I have the same organ but different biological...replicates... for example, 2 replicates of the lungs in batch 1 and 2 and the third and fourth replicate of the lungs in batch 2.
With the metadata, replicat…
updated 7.2 years ago • A
Hi everyone!
I have a problem understanding the protocol of edgeR, where a batch effect is adjusted in differential expression analysis (4.2.8).
I have also a batch effect in my samples and I have constructed...contrasts")
attr(,"contrasts")$condition
[1] "contr.treatment"
attr(,"contrasts")$batch
[1] "contr.treatment"
Is this correct?
Moreover, I have followed the…
updated 6.9 years ago • IRAIA.MAIALEN
From: Adaikalavan Ramasamy <ramasamy at="" cancer.org.uk="">
>Subject: [BioC] LIMMA: testing for batch effects
>To: BioConductor mailing list <bioconductor at="" stat.math.ethz.ch="">
>
>Dear all,
>
>We have 63 arrays that...We wish to
select
>genes adjusting for two covariates : gender (male/female) and
>experimental batch (one/…
exposure B separately) and each exposure/concentration combination has three replicates (one in each batch).
My goal is to compare each of the six experimental conditions with the control. Here my plan is to use one treatment factor...with seven levels and one batch factor with three levels.
The complication, however, is that there are more than one control per batch. Batch 1 has one control...…
updated 9.8 years ago • Ekarl2
Hi everybody,
This is a quick question regarding the DESeq2::sizeFactors() function.
To my knowledge, and I hope I am right here, this function prints out the size factor table calculated by the DESeq2::estimateSizeFactors() function, or can be used to assign a size factor table to a DESeqDataSet.
This is not working for me right now and I wonder if this is a bug or if I am doing somethi…
updated 6.8 years ago • Ben
results that are valid in the
population of interest, which usually is not plants grown in a single
batch in the green house. But how much variability should we
induce? Each batch of plants grown separately but in the same
building...different growth chambers), grown in different
labs? different universities?
In my very first Affy experiment, the investigator did the
following: 2 batches of …
updated 19.9 years ago • Naomi Altman
Hi All,
I calculated size factors for RNAseq data using the estimatesizefactor(). They were:
1a 1c 2b 2c 1b 2c 3c
1.7260367 1.8360566 0.7666819 0.7158603
updated 5.5 years ago • mankadeep2
IS Project Manager/ Day/ 40 Hrs/ Channing Division of Network Medicine - (3133887)
Description
This position includes both project management and advanced software development. The successful applicant will perform multidisciplinary work in data science, clinical trials, and cloud computing. Our group is centrally involved with the Bioconductor project, a 20-year open source/open development…
updated 4.8 years ago • Vincent J. Carey, Jr.
<div class="preformatted">I am running into memory limits and have been unable to write the
correct code to increase the allocation size. Below is my output. I am
currently running Windows XP with 2 GB of RAM. Windows Task Manager
tells me that I have over 1GB of physical memory free so I should have
plenty of room to increase.
> memory.size(max=T)
[1] 126066688
> memory.l…
updated 21.2 years ago • Kimpel, Mark W
Hi Guys,
I need a suggestion for batch variation for edgeR analysis.
Here is my samples
1) NW1
2) NW2
3) NW3
After plot MDS for NW1,NW2 and NW3, I choose to take NW1...Hi Guys,
I need a suggestion for batch variation for edgeR analysis.
Here is my samples
1) NW1
2) NW2
3) NW3
After plot MDS for NW1,NW2 and NW3, I choose to take NW1 and...for NW1, NW3, NWS1 and NWS3…
updated 7.4 years ago • drskm7
Recent ...
Replies
Comment: DECIPHER DesignProbes unable to design FISH-probes
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Comment: BiocParallel (and DESeq2) - wrong args for environment subassignment
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The DESeq2 error makes sense, as we've talked about, given that the simple `bplapply` isn't working in your setup.
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For PTM analysis, the usual quantification command dpcQuant() is replaced by dpcImpute(). Otherwise the limpa pipeline is the same as for a…
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The first step is to update to the current versions of R/Bioconductor and try again. It's possible that you have run into a bug that's alre…
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