I have rna-seq data from 5 samples of control and 5 samples of treatment, total 10 samples. The experiment were performed in different day (one control and one treatment), in total 5 days.
What would be the best way to minimize...batch effect?
Would it be possible to test each pair of control and treatment independently?
Thank you very much for your suggestions
Order by: Relevance
to Evan or Evan-LAB-People.. haha) ... I am
trying to
run ComBat to correct my methylation data for batch (which are 11
Slides)
and other covariates.
But to illustrate the problem i reduced the model to it's simplest and
picked...logBF, data=phenoData)
cBat_Mvalues <- ComBat(dat=SWANed.Mvalues, batch=Slide,
mod=
model, numCovs=NULL, par.prior =TRUE)
I get the following error:
Found 11 b…
updated 11.5 years ago • Celine Bourdon
Hi,
I am trying to model batch effect with DEseq2 but get "Error in checkFullRank(modelMatrix) : the model matrix is not full rank". My design...formula is ~ BATCH + group. Basically, I want to find gene expressed differently between different groups. I don't see the linear dependent...between BATCH and group and how to fix it. Any help would be appreciated. Thanks!
…
Hello,
I am running DESeq2 with this metadata table -
| Condition | Time | Batch |
|-----------|------|-------|
| Control | 0h | 1 |
| Control | 12h | 1 |
| Control | 24h | 1 |
| Control | 0h | 2 |
| Control | 12h | 2 |
| Control | 24h | 2 |
| Control | 0h | 3 |
| Control...Hello,
I am running DESeq2 with this metadata table -
| Condition …
updated 12 months ago • bhandary.8590
Hi, I'm new in biological analysis.
I want to use DESeq2 to do my analysis, I have batch 1 and batch 2, and the batch equals group.
![My colData][1]
If I want to remove the batch effect, should I only use **design = ~ group...condition**,
or I should use **design = ~ batch + group + condition** ?
And this is PCA result, is there any batch effect exist? Should I remove batch effect before WG…
updated 2.5 years ago • zxc741xb
and the treatments. The replicates were collected at different times, so I am assmuing there is a batch effect. I have two questions here -
1. To build the DESeq object, I am using the ~Batch + treatment + genotype + treatment:genotype...model. DESeq2 automatically converts the treatment and genotype to factor variables, but not the batch effect. So, how would it matter if Batch was considere…
updated 3.3 years ago • estafana.t98
Hello everyone,
Could I please get an opinion on whether a batch correction is recommended in my data?
Background: I have performed RNAseq gene expression analysis on 2 condition...function (DEseq2) (named "Unbatched" in the PCA plot). Subsequently, the normalised data was batch corrected using the removeBatcheffect function (edgeR) (named "Batchcorrected")
Proble…
updated 7.4 years ago • Antonio Ahn
Hello,
I have rather general question concering FDR/adjusted pvalues.
I did an RNASeq experiment (treated vs untreated cells), and analysed the data with DESeq. There I found that I had only very few transcripts...p.adj <- p.adj</pre>
b) could I use the interestingGenes set to subset the input table and re-run DESeq? Which would re-estimate all dispersions, and size factors, and e…
Hi,
I have read blogs on **how to remove batch effects in deseq2** and how to **visualize** it using **limma voom remove batch effect PCA**. I'm not sure if the batch effect was...attached output, I'm skeptical because in heat map they seem to cluster separately (with respect to batches).
Analysis: 51 samples with two batches (Batch1 includes NYGC in the label and Batch2 doesn't include NYGC in…
updated 4.6 years ago • vinisha
is in
bioinformatics,
computational biology, genomics, data-mining, and related areas.
Call
for papers: BCBGC-10, Orlando, USA, July 2010
The
2010 International Conference on Bioinformatics, Computational
Biology,
Genomics...pools and
on-site dining â all situated on 10 tropically landscaped acres.
Here, guests
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We
i…
updated 15.8 years ago • John Edward
Hi everyone,
I have a couple of questions about using ComBat from the sva package for batch effect normalisations of synthetic genetic array (SGA) data.
Briefly, for anyone who's not familiar, SGAs are a high-throughput...My first question: does anyone have any comments about the suitability of ComBat to normalise batch effects in SGA data? The colony sizes are approximately normally distribute…
updated 9.6 years ago • John Townsend
in 5 concentrations)
- a time factor with 2 levels (time of treatment)
- a batch factor with 3 levels corresponding to the laboratories that
analyzed the data
Within each dose, time and batch I've 3...merge the 3 replicates produced by each lab
into one
group with then 9 replicates (i.e. omitting the batch factor).
Unfortunately
the batch factor is very strong and introduces quite a large varian…
low training-set sizes, CMA shows an error in the
console and halts the rest of the code:
-------------------------
[snip]
tuning iteration 575
tuning iteration...say, two instead of 15 variables for classifier
generation. The R code I use should ensure that the training-sets
always have members of both classes. The code I use and the
traceback() return are further below.
I would appreciate...R…
updated 14.8 years ago • Santosh Patnaik
I would like to remove batch effects by ComBat but when we have one peptide missing for the whole batch 1 while we have data for batch 2, 3, and 4. But we...would like to incorporate this peptide in adjusting for batch effect of rest of the batches. What's the suggestion to deal with this peptide?
Thank you very much
updated 7.2 years ago • hjleeab
cluster into different groups under a certain gene signature, the samples are from two different batches so batch needs to be factored. Say I want to take a quarter of my samples that respond best to some treatment and the then...packages/devel/bioc/vignettes/limma/inst/doc/usersguide.pdf* (page 44)
```
# Let Batch Correspond to Batch Variable and Group correspond to to response group X0 is R…
the header, I get
the result but it's very hard to read. Is it possible to get this in a
readable table form with headers? Any help will be greatly
appreciated.
Thanks.
-Avoks
> data = postForm("http://www.genome.gov/GWAStudies...n First
Author/Date/ Journal/Study\r\n\t\t\r\n
Disease/Trait\r\n\t\t\r\n InitialSample Size\r\n\t\t\r\n
Replication Sample Size\r\n\r\n Re…
updated 14.1 years ago • Voke AO
allocated on my university's server.
Since the reference dataset I want to use is still a normal size for a single cell experiment, I am thinking others may have encountered a similar issue.
Does anyone have a solution?
Thanks...Code should be placed in three backticks as shown below
```r
#reading in my dataset (single cell experiment object)
PFC.merged.sce <- readRDS("sce_chi…
updated 24 months ago • elgomez
features and want to use the respective
IDs of these to extract gene data from additional tables within R.
Top table data:
Block Row Column ID Name M
A t P.Value adj.P.Val B
16415 28 9 15 I6481_cpg298I7 13_108590257...108591866
3.761146
12.28307 23.07024 1.418257e-16 4.068837e-12 27.90629
Gene info table:
V1 V2 V3 …
updated 18.6 years ago • RS Illingworth
This is a sanity-check question about how I ought to correctly use DESeq2 with knockout experiments. If I have two conditions, a control and a knockout, am I correct in putting them into one data set and then later...This is a sanity-check question about how I ought to correctly use DESeq2 with knockout experiments. If I have two conditions, a control and a knockout, am I correct in putting them …
updated 6.9 years ago • cmfield
fix this?
```r
> ref.data <- celldex::HumanPrimaryCellAtlasData(ensembl = T)
snapshotDate(): 2021-10-18
see ?celldex and browseVignettes('celldex') for documentation
loading from cache
see ?celldex and browseVignettes...celldex') for documentation
loading from cache
snapshotDate(): 2021-10-20
loading from cache
Error: failed to load resource
name: AH73881
title: Ensembl 97 Ens…
updated 4.1 years ago • immuno.dh
If you're interested in pursuing a computer hardware career, you may want to consider enrolling in a [computer hardware training institute][1]. These centers specialize in providing students with the knowledge and skills needed to work with computer...in pursuing a computer hardware career, you may want to consider enrolling in a [computer hardware training institute][1]. These centers specialize…
Case scenario
Let's assume that we have some batches of cells and they are treated with a drug in a controlled setup **(group)**. However, the experiments performed by 2 independent...labs and MDS plots showed that there is a clear batch effect **(batch)**.
```
# Matrix size
nsamples <- 12
ngenes <- 1e5
# Experimental setup
meta <- data.frame(group = factor(rep(c("…
updated 6.5 years ago • altintas.ali
<div class="preformatted">Dear Colleagues
We invite you to participate in the ninth international conference for
the
Critical Assessment of Massive Data Analysis (CAMDA2009),
http://www.camda2009.org, which will be held in Chicago, IL, USA from
Oct. 5
to 6, 2009.
This year's topic is about next-generation sequencing. CAMDA2009 will
have
two tracks.
Track I: Analysis based on a common con…
updated 16.3 years ago • Pan Du
In the *Feature selection across batches* section of the `simpleSingleCell` *Correcting batch effects* [vignette][1], genes with positive average (across batches...What is the reasoning behind that? Why aren't genes with positive biological variance in any batch selected instead?
[1]: https://bioconductor.org/packages/release/workflows/vignettes/simpleSingleCell/inst/doc/batch.html
updated 6.3 years ago • Angelos Armen
Hi, I'm relatively new to bioinformatics, and have been following the Galaxy pipleine for my RNA seq data. At this stage, I have featureCounts count tables.
In one one of the DEG experiments, I have to compare WT baseline data (2 males + 2 females) vs WT at 1h (2 males + 2 females). I am using "Timepoint" as my primary Factor, and the 2 groups mentioned before as my Factor Level 1 and 2 respe…
analysis with RnBeads, the analysis.log file reports warning messages concerning the tracks and tables module, as reported following:
STATUS STARTED Exporting sites
2021-03-07 15:36:10 2.6 STATUS STARTED Creating Track...Hub -- bigBed
2021-03-07 15:36:10 2.6 WARNING Skipped conversion bed -> bigBed for region type si…
updated 4.8 years ago • Federica
have animals which learn a task on only 1 side of the body. I then harvest CNS tissue from the trained and untrained sides. Gene expression due to learning is then identified by comparing the trained and untrained...be clear, I'm interested in relating memory scores to the log-fold-change scores (the comparisons of trained/untrained), though I suppose it could also be possible…
updated 8.8 years ago • Calin-Jageman, Robert
surfaces: water, glass, PET and PE
I have 5 locations: A, B, C, D and E
I also seem to have a batch effect as locations B&D was ran on the sequencer a different day than A,C,E.
I was trying to correct for this by designing...that incorporated the location as an effect and then duplicate correlation to compensate for the batch effect. See code below:
```group<-factor…
updated 5.0 years ago • Katherine
Hi,
I’m working with RNA-seq dataset and I’m using DESeq2 (v 1.10) with complex experimental designs.
I have several variables to work with :
* Visite : 2 levels (before and after treatment)
* Patients : Responders and Non-responders, female and male
* Batch : paired samples are in different batches
For example :
<table border="0…
updated 8.2 years ago • rejane.troudet
I'm trying to compare gene expression levels of a certain cell type generated in-vitro to expression of multiple cell types in-vivo using DESeq2. The data may be described as in the following experimental design table.
```r
CT = c(sprintf("iCTa%d",1:4),sprintf("nCTa%d",1:6),sprintf("nCTb%d",1:2),sprintf("nCTc%d",1:2))
LB = c(rep(4,"LAB_A"),rep(10,"LAB_B"))
SMP = c(sprintf("A_SMP%d",1:4),sprintf("…
such large relative effect sizes (and low FDRs) when it looks like the expression is actually pretty much unchanged in the raw count data?
For example, looking...at the table produced by `fData(jscs)`, the 2-exon gene WBGene00015769 has these results:
```
geneID featureType countbinID testable...254.4281 0
```
Note the Log2FC (5.5) for exon E001 and the VST-transfo…
updated 6.0 years ago • stuart
I'm back from a hiatus from expression analysis and am faced with analyzing a messy gene expression experiment. Any advice would be very appreciated.
The samples consists of multiple normal and diseased regions from multiple...individuals. The number of samples varies between donors:
<table border="1" cellpadding="1" cellspacing="1" style="width:300px">
<thead>
<tr>
<th sco…
updated 8.0 years ago • Tore
I realize that the topic of batch effect removal in RNA-seq has been addressed many times. I am not sure if this particular aspect of it was, but I may have...Specifically, there is a note:
> If there is unwanted variation present in the data (e.g. batch
> effects) it is always recommend to correct for this, which can be
> accommodated in DESeq2 by including in the desig…
updated 5.1 years ago • igor
notes from the birds of a feather session at the Bioconductor Developer Day 2017-07-26
## __Writing papers in Rmarkdown, BiocStyle... (and books, posters)__
__Multi-panel figures __
<span style="background-color:transparent...also define your own CSS); xtable</span>
<span style="background-color:transparent">interactive tables: DT CRAN package, an interface to JavaS…
div class="preformatted">Hi everybody,
I would like to know whether it is possible to compare to tables for
certain
parameters.
I have these two tables:
gene table
name chr start end str accession Length
gen1 4 646752 646838...MI0011290 114
gen4 2L 2737568 2737661 + MI0017696 93
...
localization table:
Chr Start End …
div class="preformatted">Hi,
Is it possible to correct for batch effects in limma when doing a
paired analysis? I have pairs from two
runs Batch 1 and Batch 2. There are no pairs where...one is in Batch1
and the
other in Batch 2. If I enter the Batch no. into the design matrix,
no coefficients are generated as there is no difference between run
no
in a dataset of 6 tests and 6 control samples. The cDNA library preparation has been performed in 2 batches. The second batch contains only 2 samples and both of them are in the control group. When I am trying to correct for the...batch effect (~ batch + treatment), the results are not different than when the effect of batch is not included (~ treatment). As there
updated 6.1 years ago • Mehdi Emam
div class="preformatted">Dear list,
Now I am using sva to remove batch effect in my mircoarray data. First
I used combat to remove know batch effects. The combat can output a
new expression...matrix without batch effect, then I used sva to remove
unknow batch effect, but it seems that sva can not output a new
expression matrix. sva take...the surrogate variables into the test. How
can I let s…
The experimental design is 3 conditions, with 2 samples in each condition.
Therefore, my coldata table looks like this:
```
Samp_ID Condition
S1 Cond_1
S2 Cond_1
S3 Cond_2
S4 Cond_2
S5 Cond_3
S6 Cond_3
```
S1 is showing a batch effect...my PCA plot comes out like this.
![enter image description here][1]
I wanted to co…
updated 2.5 years ago • Jung E. Ji
Hello everyone,
I am submitting an R package to Bioconductor. I have 2 vignettes and the size is 5.7M and 2.3M respectively. BiocCheck requires the package size is within 4M, so I cannot pass the check.
The vignette...size is so large since it contains many png images. I have reduced the resolutions of the images and moved all images to github...In the Rmd I inserted links to these images,…
updated 6.6 years ago • zhang.jianhai
in this image:
![enter image description here][1]
I was wondering using the formula ```design = ~ batch + condition``` would be sufficient enough to control for batch effect considering the fact that the control group is not...represented in the other batch. How should I proceed with further analysis? Surprisingly, Limma was able to somewhat correct the data to cluster broadly
updated 21 months ago • sap275
preferred), preference for fields
of computer science, bioinformatics, statistics, or biotechnology.
Experience and Training: At least four years of experience with
designing, deploying and administering computational infrastructures...or biotechnology.
Alternative degree fields may be considered/accepted if accompanied by
equivalent experience. Experience and Training: At least two years'
exper…
updated 13.7 years ago • Jenny Drnevich
matrix of 1208 samples (1095 tumor and 113 normal) downloaded from TCGA. I know there are 3 batch effects: type, plateId and TSS. I've tried to correct for them with Combat but I need a little help with the model.matrix...Is there anyone who can help me? I'm a student. Thanks in advance. The code is:
<pre>
batch<-as.data.frame(cbind(samples,plateId,group,TSS),as.is=T)[,…
updated 7.5 years ago • Fp
I am trying to perform differential RNA-Seq analysis from plasmodium species. I am using R command lines and I was trying to include the estimates of cell stages obtained from CIBERSORT deconvolution alongside batch effect estimate using RUVr.
I managed to do the differential analysis with the code below just by including the batch effect estimate but I found a difficulty including the proportio…
updated 18 months ago • ij283
not clear on what/how to do this.
Here is my experimental setup:
Array Param1 Param2 Rep Batch
1 H 4 1 1
2 H 4 2 2
3 H 4 3 2
4 H 20 1 1
5 H 20 2 2
6 H 20 3 2
7 H 37 1 1
8 H 37 2 2
9 H …
updated 18.4 years ago • Nathan Haigh
Hello All,
I have an RNA-seq dataset and I've performed PCA analysis to check batch effect using package edgeR. and have used raw counts from cuffnorm output.
here is my code
library(edgeR...dge1)
logCPM1 <- cpm(dge1,log=TRUE,prior.count=5)
batch=c(rep("batch1",8), rep("batch2",8))
&…
updated 7.9 years ago • cvu
Dear List,
I have microrarray data where condition is completely confounded with
a time
batch effect. When doing a PCA on the RMA normalized data, the first
principal
component separates clearly the two batches...What option do I have when I still want to compare different
conditions across
batches?
As far as I understood I can't dissolve this batch effect neither with
limma nor
with e.g. ComBat…
div class="preformatted">Dear list,
In my mrcroarray data, there is batch effect. But I am not very clear
what kind of batch effect in it. I want to using PCA to remove batch
effect, but I am confused...how to from the raw expression data to get a
new expression data without batch effect in it.
Any suggestion will be welcome.
Thanks.
</div
updated 14.0 years ago • Fabrice Tourre
browser showed no sign of excessive noise (see picture for example). However, samples from second batch were sequenced much deeper (bottom, ~25 million reads) than ones from first batch (top, ~7 million reads).
<img alt="IGB view" src...From this picture, we can see that samples for control condition ('Temp1', common between 2 batches) do not cluster together between batches (small VS large p…
updated 7.2 years ago • rfenouil
Dear All,
I would like to clarify certain doubts and have opinions on the rna-seq data analysis I have been doing.
I have RNA-Seq data from paired experiment i.e I have treated and untreated data for the same tissue which is sequenced in the same batch. I have data from 40 different biological samples ( 40 treated and 40 untreated ) and more to come. This data tends to be heterogenous, so I am …
Hi Michael,
I'm trying to remove the batch effect from my samples doing like this:
APPOGGIO:
<pre>
Well Barcode day bioRep RAcond TNx techRep
ATTACT B4 ATTACT D5...Hi Michael,
I'm trying to remove the batch effect from my samples doing like this:
APPOGGIO:
<pre>
Well Barcode day bioRep RAcond TNx techRep
ATTACT B4 ATTACT D5 n1...pre>
v…
updated 7.2 years ago • santamariagianluca
with Limma? Any suggestions on what could be happening for the P-values to be so weird? In case my n-sizes were too big, any ideas on other tools I could use for differential expression analysis of such a dataset?
Thanks in advance...My code:
```r
#My data matrix looks something like this:
data_norm[1:5, 1:5]
#This is my n size:
table(metadata_filtered$Fiber_type)
#First I created…
updated 3.6 years ago • roger.moreno.justicia
statistical methods for detecting differentially
expressed genes from RNA-seq data
this is a good paper to compare them
but who can give more comparision ?
--
shan gao
Room 231(Dr.Fei lab)
Boyce Thompson Institute
Cornell University
updated 13.1 years ago • wang peter
Deseq2 is required a count metric. However, after I look into my count data, I would that there is a batch effect in my count data.
![As from you see in the image, the image shown the total read count of the data batch 2 (high read count...count before using in Deseq2 analysis.
What is the best option in my analysis,
(1) Performing batch normalization using Combatseq --> Deseq2 --&am…
updated 2.7 years ago • suphamon.j
Why library sizes in the DGE object are different from original library sizes? And which library sizes should be used in differential...expression analysis?
![Original lib sizes][1]
![Lib sizes after creating DGE object][2]
```
dge <- DGEList(counts = Counts,
group = sampleInfo$Group,
genes = genes[which(rownames
updated 20 months ago • Shaimaa Gamal
div class="preformatted">This is to gauge interest in a Bioconductor training
class in Boston, 13-15 Jul 2006 (Thurs-Sat). Topics
will be, roughly, Day 1: R background; R/bioc container
and workflow overview...U affiliate.
If you are interested in attending, please send a note
with header "Boston Bioc Training 2006" to
stvjc at channing.harvard.edu. I will decide whether
to hold the course …
updated 19.5 years ago • Vincent J. Carey, Jr.
Hii,
I have 3 batches of samples that belong to 3 conditions/treatments i.e.. batch1(control), batch2(disease stage1), batch3(disease stage2...which belong to the same microarray platform and same tissue.
1) Is there a way to find batch effect for this case ?
2) If so, how can i perform batch adjustment in this case ?
3) Which method should i use to retain biological...variation among the bat…
updated 9.0 years ago • vinnu260
I have samples for two groups: males with disease (n=114) and females with disease (n=65) (male or female set as condition). I wanted to assess differential gene expression. My results show that a male-specific gene (SRY) has a negative log2fold change when females are set as reference meaning (if I am understanding correctly) that SRY was downregulated in males compared to females. SRY gene s…
updated 21 months ago • hmillike
div class="preformatted">Dear Jana,
Unless there is a strong batch effect between the two replicates of
the
entire experiment, there is no need to account for this level
explicitly.
So...duplicate (so each sample is on two arrays). For each
comparison, I have also repeated the exposure experiment twice (i.e.
the actual experiment was replicated, not the array, so new biological
samples). So …
updated 12.3 years ago • Gordon Smyth
<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…
Recent ...
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