div class="preformatted">All,
A collaborator has approached me with a situation in which a batch is
completely confounded with treatment for
affy gene expression data.
I am wondering if there is anything reasonable...wondering if anything can be done with
control genes.
Does anyone have any suggestions, pointers to papers, or a template
script? The key feature is, of course, the complete
co…
Order by: Relevance
to do the following things:
First, do normalization (logCPM) in total samples to check wether batch exists then split the matrix into training set and test set.
Second, use limma to find different genes or windows in training...set.
Third, select important features in different genes and windows with elasticnet in training set to construct binary classification models and make prediction…
updated 4.3 years ago • hxlei613
is related to some processing steps in the
laboratory (ChIP-experiment).
My first general question is how do you deal with batch effects? I
found
not much about it in the archive.
I proceeded...limma for computing oligos with differential intensities
between
two classes. Adding a factor for batch effects is easy and reduces the
R^2 of the gene-wise models in my case noticeably.
I am more worri…
updated 18.2 years ago • Hans-Ulrich Klein
genes between different groups in RNA-seq data. I have 55 samples that were prepared either in batch 3, batch 4 or batch 6. These samples represent 4 groups (NR, NT, P, F). When I checked the MDS plot, all the samples were separated...by group and by batch, so it seems that the batch effect should be corrected. The problem is that one group (group F) has only 4 samples, which were...all prepared …
updated 6.5 years ago • Laura
limma)
library(sva)
library(bladderbatch)
pca_any <- function(counts, colorby, label, name, size, scale){
pcax = prcomp(t( counts ), scale=scale)
pcvar = pcax$sdev^2/sum(pcax$sdev^2)*100
p = qplot(pcax$x[,1],pcax$x[,2], main=paste(name, ', scale...label) +
labs(colour='groups')
png(file=paste("pca-", name, ".png", sep=''), res=200, width=size, height=size)
print(p)…
updated 9.4 years ago • nsakabe
I'm currently analyzing 4 microarray experiments in an integrated manner. For this, I'm using limma accounting for the batches through the design matrix:
<pre>
design...I'm currently analyzing 4 microarray experiments in an integrated manner. For this, I'm using limma accounting for the batches through the design matrix:
<pre>
design <- model.matrix(~0+Class+Batch, data = p…
updated 8.4 years ago • tcalvo
them as depicted in chapter 5.4 of ["A guide to creating design matrices for gene expression experiments"][1].
During my analysis, I tried to remove one or more of these features, and it affected the number of DEGs greatly...limma pipeline two times:
- **Without the stub**:
- The formula is "~0 + Feature + batch + Age + Sex"
- Feature is a factor with levels are A, B, C
- …
I am trying to get a table of GSE data I have but I get the following error:
"Error in (function (classes, fdef, mtable) :
unable to find an inherited method...for function ‘Table’ for signature ‘"GSE"’ "
The code in R studio is this:
library(GEOquery)
gds <- getGEO(filename = "GSE7535_family.soft.gz")
geData...lt;- Table(gds)
sessionInfo( )
R version 4.1.0 (2021-05-18)
Platfor…
updated 4.4 years ago • pedram_torabian
Hi everyone,
I'm working on RNA-Seq datasets containing 22 samples from 3 batches. I used mm10 as the reference genome and generated the count table from the BAM files using GenomicAlignments package...Hi everyone,
I'm working on RNA-Seq datasets containing 22 samples from 3 batches. I used mm10 as the reference genome and generated the count table from the BAM files using GenomicAlignments pac…
updated 10.1 years ago • AB
metadata below). However, 1 of the cell types (HCT116) was done in a different lab and shows a stark batch effect between its two replicates, while the other 2 cell types have a more muted batch effect between their two replicates...Overall, I see the best precision with a known set of gene targets when using the native DESeq2 batch correction in HCT116, but the other two cell types show a small …
updated 2.3 years ago • Hope
In the `simpleSingleCell` *Correcting batch effects* [vignette][1] spike-ins are available. What is the recommended workflow in the absence of spike-ins? I understand...that `makeTechTrend` should be applied to each batch separately and then genes with positive biological variance in any batch should be selected before calling `multiBatchNorm...a Poisson distribution (as assumed by `makeTechTrend…
updated 6.3 years ago • Angelos Armen
Hi all,
I have an RNAseq experiment confounded by batch effect. Its a time-course design with the following setup:
time batch
1 0 1
2 0 1
3 1.5 1
4 1.5 1
5 1.5...3Dvs0, but 3 and 3D are two different treatments at the same time point, and they are in different batches, so its impossible to separate biological effect from the p…
updated 6.7 years ago • gtechbio
know the design is terrible, but this is what I have to work with ;)
Question 1: can I remove the batch effect between 2 groups if their samples do not share a batch, but some of their samples share a batch with a third group...groups are different genotypes, batches are different experiments)
Example: I want to compare group gA (samples s1, s2, s3) with group gC (samples s8, s9, s10, s11). The…
some things out. I followed the OSCA book for my analyses but I am still unsure as to when to apply batch corrections.
I have four experimental groups (three mouse brains pooled per group), but I understand correctly, during...the actual snRNAseq experiment (done by a collaborator) there were four Illumina libraries prepped (one per group, same protocol for all done at...and thus I got four fi…
updated 22 months ago • NeuroDaniel
hybridised about half of the samples when he
realised he needed more Affymetrix chips.
The second batch of chips arrived with the instruction to add DMSO in
the hybridisation cocktail, which he followed. The first batch did...not
have such instruction. Therefore we believe that the two batches are
not
directly comparable. A posting to GeneArray mailing list had a reply
(http://bfx.kribb.re.kr/ge…
updated 21.0 years ago • Adaikalavan Ramasamy
a centroid based classifier. This is my workflow
1) In order to do this with a valid sample size, I merged multiple datasets from several platforms. Plotting a PCA revealed an obvious _dataset effect_. After checking...in <http://biostatistics.oxfordjournals.org/content/17/1/29>) I decided to use ComBat for batch effect correction. Based on the after-ComBat PCA, things worked o…
updated 7.3 years ago • jmsendoya
at the differential gene expression effect of a certain treatment or condition while correcting for batch. However, I am not sure how to set up a proper design formula to do this.
My data looks like this (simplified):
```
batch treatment...between 15-19 replicates of each of these 4.
Now, if all of these where processed in a different batch, I would use the following design:
```…
updated 5.8 years ago • l.rijnberk
Hi,
I have some 450k data for ~1000 samples. I want to use ComBat to adjust for 2 known batches. I would like to adjust for Age\_Group and Sentrix\_ID (cf. example below). My variable of interest is Sample\_Group. I don...accordingly to old posts) and what to put in the model.matrix. I was thinking to do:
First:
<pre>
batch <- pheno$Age_Group
mod <- model.matrix(~as.facto…
Dear Bioconductor community,
i have some gene expression microarray data, on which i would like to fit a machine learning methodology and construct a classifier regarding a binary outcome(Disease status). Although from literature and various papers i have found various packages and methodologies in R, as i would like also to add additional continuous variables alongside...a classifier regarding …
updated 10.2 years ago • svlachavas
hsin lin <yu-hsin.lin@stonebow.otago.ac.nz>
To: maechler@r-project.org
Subject: R and Bioconductor training
Date: Wed, 13 Aug 2003 15:31:01 +1200
Hi,
Is there any R and Bioconductor training in Taiwan in the near future?
Thanks,
Yu
updated 22.3 years ago • Martin Maechler
Hello,
I'd like to combine two microarrays (same platform and chip) - two different experiments.
Currently I have results of two experiments (Affy U133 Plus 2.0) performed in two different labs. I'd like to combine...Hello,
I'd like to combine two microarrays (same platform and chip) - two different experiments.
Currently I have results of two experiments (Affy U133 Plus 2.0) performed in two…
updated 7.0 years ago • Adam_M
way to define the design in the EdgeR workflow is for a pairwise analysis, while also accounting for batch effects, in terms of the design <- model.matrix(~x+y) term.
The setup of our experiment is quite simple: we have 18...cases who had blood RNA-seq before and after treatment, but these samples were run in different batches. Therefore, we expect batch effects and wou…
updated 10.9 years ago • cinderelliedoll
I have a RNASeq paired-end data from two batches (8 samples from batch1, and 7 samples from batch2). After alignment using TopHat2, then I got count ...I have a RNASeq paired-end data from two batches (8 samples from batch1, and 7 samples from batch2). After alignment using TopHat2, then I got count using HTseq-count, and FPKM…
B.22 - B.0)-(A.22 - A.0) ?
This design is completely described in the paragraph “9.7 multi-level experiment” of limma user’s guide.
My problem is that the samples were processed in batches before I was in charge of this study...t2 p11 B6
23 A t1 p12 B6
24 A t2 p12 B6</pre>
The last batches B5 and B6 have the same proportion B/A, here : 1/3 a…
updated 10.0 years ago • eleonoregravier
of bioinformatics workflows and pipelines
- Provide bioinformatics consulting and software training to junior researchers
**Required qualifications:**
- University degree or postgraduate training in computational...biology / bioinformatics
- Extensive and broad experience in the computational analysis of omics data
- Solid programming skills and familiarity with Linux compute clusters...De…
updated 5.0 years ago • sergisayolspuig
am a novice and I am interested in comparing two kind of cells coming from different RNA sequencing experiments published.
The design would be something like the following:
sample cell batch
1 type1 1
2 type1 1
3 type1 1
4 type1...8 type2 3
9 type2 4
10 type2 4
Now, naturally I cannot model del batch effect with …
updated 6.1 years ago • MT
in using RUVSeq::RUVs() as it appears to be the only published and packaged method for correcting batch effects using technical replicates profiled across batches.
However, I must be doing something wrong because I can...t get it to work.
I have a non-ideal experimental design with two batches:
* Batch 1 contains 40 samples with condition A + 12 samples with condition B
* Batch 2 conta…
of Science, Israel
Erik Sonnhammer, Stockholm University, Sweden
and about 200 other PC-members
* *
*Paper and Poster Submission Details:
*Authors are invited to submit original research contributions or
experience reports...in English.
Paper registration and electronic submission will start in August
2006.
Submitted papers will be carefully evaluated based...on originality,
significance, te…
also be held at the same time and place (each
conference has its own proceedings). We invite draft paper
submissions.
See the website: http://www.iiconference.org for more details.
Proceedings will be submitted for indexing...conference will be
held every two years to make it an ideal platform for people to share
views and experiences in AI and related areas.
Sincerely,
Venkateswara Rao
Organ…
updated 12.8 years ago • Venkateswara Rao
div class="preformatted">some have asked me about pooling in microarrays. a paper by
Kendziorski,
et al can be found here
http://www.bepress.com/jhubiostat/paper46/</div
updated 21.4 years ago • Rafael A. Irizarry
Hello, I have used the RUVg function in RUVSeq to successfully remove the batch effects in my two groups of samples. Both are controls so I am not concerned about removing any biological significance...have created RLE and PCA plots that have the demonstrated the desired effect, now how do I output a table of these batch effect free normalized counts?
I read here: https://support.biocon…
is one explanation. For example -- not that this has to be
the
explanation in your case -- in some experiments with case and controls
not
perfectly balanced across batches, one might see significance
'wrongly'
associated...with the condition when not including a batch effect, but
when
including the batch effect, the effect size for condition goes away.
Adding covariates, in both GLM and...simple…
of the
samples. For this I used the minfi package. Unfortunately, the assays
were done in 2 batches and there is a clear batch effect. I looked
into Combat and SVA to remove the batch effect. As far as I
understand, to use...I need to have a
phenotype/variable of interest. In the tutorial ("The SVA package for
removing batch effects and other unwanted variation in high-throughput
experiments ??? …
updated 13.5 years ago • Guest User
events:
Biological Interpretation of Next Generation Sequencing
[http://www.ebi.ac.uk/training/course/Bio\_NGS2015](http://www.ebi.ac.uk/training/course/Bio_NGS2015)
Monday, March 23, 2015- Friday, March 27, 2015...EMBL-EBI, Hinxton, UK
Advanced RNA-Seq and ChiP-Seq Data Analysis
<http://www.ebi.ac.uk/training/course/RNA2015>
Monday, May 11, 2015- Thursday, May 14, 201…
Hi
i have a set of RNAseq data with unbalanced batch effect (see table below). Batch 1 was made of single indexed kit and sequenced at time 1, while batch 2 was made of dual indexed...kit and sequenced independently from batch 1.
<table border="0" cellpadding="0" cellspacing="0" style="width:455px">
<tbody>
<tr>
<td> </td>
<td><code>s…
updated 7.3 years ago • sckinta
<div class="preformatted">Hello,
I have ~100 RNA seq-samples from the same organism, but they include
different experiments (each experiment of 6-16 samples). I would like
to put all together into our RNA seq pipeline, that includes mapping,
htseq count and DESeq. Differential expression comparisons will be
done of course only between samples of a single experiment (due to
possible batch …
updated 11.6 years ago • Guest User
Discover excellence in Openshift training at WebAsha Technologies, a leading Openshift Training Institute. Our carefully designed program will teach you...orchestration platform in the industry.
[https://www.webasha.com/courses/openshift-online-training-institute-certification-exam-center][1]
![enter image description here][2]
[1]: https://www.webasha.com/courses/openshift...online…
updated 2.2 years ago • WebAsha
div class="preformatted">Dear List,
For high-throughput experiments (mircroarray, RNASeq, etc) with many
batches of samples, as a routine procedure, we are suggested to apply
Combat...SVA, PCA or PEER method to remove batch effects and hidden
variables before any downstream analysis. But in terms of specific
steps, I
have listed the following...method is the best or other suggestions?
Method…
updated 11.4 years ago • shirley zhang
WebAsha's OpenShift Course Training is the most comprehensive and up-to-date training available for OpenShift. Our instructors are experienced OpenShift...the confidence you need to master OpenShift.
[https://www.webasha.com/courses/openshift-online-training-institute-certification-exam-center][1]
![enter image description here][2]
[1]: https://www.webasha.com/courses/openshift..…
updated 2.2 years ago • WebAsha
I have RNAseq from three treatments (A, B, C), each with biological replicates ran in two batches (batch1 with A & B; batch2 with C). Unfortunately, the batch effects are fully confounded with the condition (e.g., to compare...A vs. C). Here, I understand it is impossible to separate the batch effects from the treatment, regardless of what statistical method I use. I thought of methods su…
updated 5.6 years ago • bhakti.dwivedi
Hello,
I have a fair amount of experience using DESeq for relatively simple study designs (ie: ~ batch + genotype to look for effect of genotype while controlling...sources of noise. Ie: How does my GOI regulate gene expression?** The first source of noise is batch effects due to experiments (4 samples were prepared initially: "old"; 12 samples were prepared later "new"), and the second...was …
updated 6.3 years ago • rachellcosby
do - illustrated on bladderbatch data
1)batches in my actuall dataset
<table border="0" cellpadding="0" cellspacing="0" style="width:256px">
<tbody>
<tr>
<td>batch</td>
<td>Control...td>
<td>Cond1</td>
<td>Cond2</td>
</tr>
<tr>
<td>batch 1</td>
<td>8</td>
<td>0</td>
<td>0</td&…
updated 10.9 years ago • AdamJ
In DiffBind when you draw a heatmap based on an experiment with a small number of observations the labels are quite large and only a few characters fit on the screen. ...As the number of observations goes up the font size goes down and more characters are printed. I'm' wondering if I can gain control of the font size in the labels, to enable...me to see more characters even in e…
WebAsha's Online OpenShift Training Institute is the perfect place to learn OpenShift from experts. Our training program is delivered online, so you...and from anywhere in the world. We also offer a variety of learning options, including live online training, self-paced online training.
[https://www.webasha.com/courses/openshift-online-training-institute-certification...enter image descripti…
updated 2.2 years ago • WebAsha
Hi everyone,
I have some doubts about the removeBatchEffect function from the Limma package.
I am working on association of expression data (RNAseq) with a continuous phenotype variation (instead of a case control experiment), and I am using this function to remove the batch effect.
Can I use the values for my continuous phenotype in the design matrix?
The model I used so far wa…
updated 7.1 years ago • dressa_ol
I'm trying to adjust batch effect using `deseq2 limma::removeBatchEffect` and also `Combat-Seq`. With limma version, I can clearly see the batch effect...Samplebatch + cond)
dds <- DESeq(dds)
dds
dds$batch <- as.numeric(dds$Samplebatch)
dds$cond
dds$batch
## vst after adding batch information
vsd_abc <- vst(dds, blind = FALSE...data), batch=batch, group=cond2)
dds <…
updated 2.7 years ago • vk
<div class="preformatted">Hi,
I am trying to set up a two channel analysis using cellHTS2.
I have cell line X. X has control (C) and experiment (E) conditions.
The screen uses 3 x 96 well plates and C and E have 2 replicates each,
hence C and E have 6 plates each in...trying to set up a two channel analysis using cellHTS2.
I have cell line X. X has control (C) and experiment (E) conditio…
The Department of Biostatistics at Virginia Commonwealth
University
has a T32 training grant supported by the National Institute
of
Environmental Health Sciences entitled "Integration of
Chemical...to fill a post-doctoral position
with
salary ranges from $31,000-$51,000, commensurate with experience.
The
post-doctoral trainee will collaborate with statisticians in
m…
2. 5 known conditions.
3. 4 biological replicates per condition.
4. To be run in a single batch.
Questions:
1. Are there possible advantages to normalizing RUV as distinct from NanoStringNorm
on this small, one-batch...dataset?
2. I have read the recent paper on RUV-III as applied to Nanostring:
https://www.ncbi.nlm.nih.gov/pubmed/31114909
Should RUV-III be applied to a diff…
updated 5.6 years ago • raf4
div class="preformatted">Hi Everybody,
I am analysing Illumina micro-array data and seem to have batch
effects
(plots attached) in my data. For batch effect removal I am using
Combat
from 'sva' package. This is my sample info file...Array.name Sample Stage Condition Batch
P4_A 1 P4 Test 1
P4_B 2 P4 Test 1
P4_C 3 P4 Test 1
P30_A 4 P30 Te…
updated 4.6 years ago • Bade
tuxedo pipeline for the analysis (HISAT2, String tie and Ballgown). Some of the samples within the experiment were sequenced in different batches. Can you please advise me on which step should I include the batch effects
updated 7.2 years ago • amy16
div class="preformatted">Dear all,
The paper on IRanges, GenomicRanges and GenomicFeatures (Software for
Computing and Annotating Genomic Ranges) has been published...through
PLoS
Computational Biology[1]. Please cite the paper whenever basing
software on
the infrastructure, or making direct use of it data analyses. A big
thanks
to the co-authors
updated 12.3 years ago • Michael Lawrence
in the fields of genomics in France (note necessarily
french speaker)
I'm trying to setup a training session for a few people. Please if you
offer this type of service feel free to contact me directly.
thanks,
david
</div
updated 14.4 years ago • David
Guide, this can be done by adding batch as a
confounding factor to the design matrix used by voom and limma fit.
However, when I run an MDS plot on batch using the...voom results, it's
still showing a clear batch effect. What am I missing? What is the
best way to correct for and test for batch effect after correction?
In the design matrix...datamat,genes=rownames(datamat))
> y = calcNo…
updated 11.9 years ago • Heather Estrella
vs paired end). I am trying to model the batch effect in DESeq2 in order to account for effects by batch but im running in to trouble and am unsure why:
I have two datasets...specified.
As far as i am aware these are not the same as batch is simply batch 1 and batch 2, while the groups has multipls groups, control, trt 1, trt2, trt3 etc...
I guess the first question...how to overcome t…
updated 6.2 years ago • A
Hi,
I am using DESeq2 to search for highly variable genes. My experiment includes cells from 3 different human donors, they were planned as biological replicates and all treated under...Hi,
I am using DESeq2 to search for highly variable genes. My experiment includes cells from 3 different human donors, they were planned as biological replicates and all treated under the same condition. As …
updated 5.8 years ago • f_pardow
recount team,
First of all, congratulations this great resource, which I am regularly using for training and research.
I have a problem with several studies (e.g. SRP042620), where the structure of the pheno table extracted
updated 6.0 years ago • Jacques.van-Helden
results. However, I would like to get some clarification on the values reported in the Stats Table, so I can be sure I interpret the results correctly.
In generalized terms, EGSEA runs gene set scoring based on logCPM...by their p-values. These individual ranks are reported in the right hand part of the EGSEA Stats Table. To find a 'consensus' across the different tools, EGSEA then uses variou…
Hello,
I have the following RNA-seq experimental design:
- Control: 3 biological replicates from ther first sequencing + resequencing from the 3 same samples
- Treatment1: 3 biological replicates from ther first sequencing + resequencing from the 3 same samples
- Treatment2: 3 biological replicates from ther first sequencing + resequencing from the 3 same samples
* The resequenc…
updated 4.1 years ago • ary.lech
Hello! I have a question about correcting for batch effects prior to differential gene expression analysis with limma. I've read that batch effect correction functions...such as ComBat should not be used prior to differential expression analysis in limma, and that batch effects should be accounted for in linear modeling instead. However, in my case a batch effect and disease eff…
updated 8.5 years ago • adscheid3
Recent ...
Replies
Comment: DECIPHER DesignProbes unable to design FISH-probes
by
Erik Wright
▴
150
Are the sequences aligned (i.e., the same width) before running `TileSeqs()`?
Comment: BiocParallel (and DESeq2) - wrong args for environment subassignment
by
Michael Love
43k
BTW, I tested with no issue on MacOS ARM on our previous github issue.
Answer: DESeq(dds, parallel=TRUE) wrong args for environment subassignment
by
Michael Love
43k
The DESeq2 error makes sense, as we've talked about, given that the simple `bplapply` isn't working in your setup.
Maybe give the traceb…
Answer: PTM analysis in LIMPA
by
Gordon Smyth
53k
For PTM analysis, the usual quantification command dpcQuant() is replaced by dpcImpute(). Otherwise the limpa pipeline is the same as for a…
Answer: problem reading bam files into nucleR
by
James W. MacDonald
68k
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…
Awards
• All
Popular Question to
Gordon Smyth
53k
Commentator to
sina.nassiri
▴
130
Popular Question to
Hervé Pagès
16k
Popular Question to
jared.andrews07
▴
30
Locations
• All
United States, 8 minutes ago
United States, 1 hour ago
Seattle, WA, United States, 2 hours ago
United States, 3 hours ago
Barcelona, Spain, 5 hours ago
United States, 8 minutes ago
United States, 1 hour ago
Seattle, WA, United States, 2 hours ago
United States, 3 hours ago
Barcelona, Spain, 5 hours ago
Traffic: 1024 users visited in the last hour
Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by the
version 2.3.6
version 2.3.6