Due to memory problems, I am using a remote PC with 2Gb of RAM with
a
Linux OS (I have very little experience using X OS).
Everything is OK, but I can?t plot the image obtained with AffyPLM
with
this command:
> image(Pset,which...gt;image(Pset,which=1)
Error in plot.new() : figure margins too large
B) Problems with the file size:
>postscript("QC.ps")
>par(mfrow=c(7,3), ma…
Order by: Relevance
We are seeking to appoint a highly motivated and experienced statistical bioinformatician with experience in a relevant discipline such as statistics, mathematics, computer science, computational biology or genetics...skills toward mass spectrometry based experimental data. The appointee will have solid mathematical training as well as strong programming and data analysis skills. Familiarity with…
updated 5.2 years ago • Laura
I am comparing three groups A, B and C and they are in 3 batches of library preparation. In the
| Sample Name | Condition | Batch |
|-----------|-------|------|
| 1 | A | 1 |
| 2 | A | 1 |
| 3 | B | 1 |
| 4 | B | 1 |
| 5 | A | 2 |
| 6 | A | 2 |
| 7 | B | 2 |
| 8 | B | 2 |
| 9 | C | 3 |
| 10 | C | 3 |
| 11 | B | 3 |
| 12 | B | 3 |
Is the group...C being in only batch 3 confound…
updated 21 months ago • prabath_meemaduma
Hello everyone,
I am doing a big RNA seq experiment and I was looking for the expression of a particular gene but I did not find it in my DESeq2 output table. I found this...anyone explain this to me? I have the output which concerns me shown below, first part of the DESeq2 table, then the salmon counts. It regards gene m00115031
Thanks
baseMean log2FoldChange lfcSE stat pvalue pad…
updated 3.9 years ago • tomtom
it says
> For unbalanced batches (e.g. the condition groups are not distributed
> balanced across batches), the design argument should be used, see
>...for details.
As far as I understand, I can check whether the design is balanced by looking at
table(Condition, batch)
BMI_group
Condition Normal Obese Overweight
Negative 8 …
data normalised
by RMA and produced a predictor. We would like to test this predictor
on a training set we have. Is it possible to RMA normalise the test
dataset so that the probes have the same distribution as the...training
dataset without normalising all the data together? Our concern is
that if you normalise them all together then this
updated 14.1 years ago • Daniel Brewer
are Agilent 244k, Affy
SNP 6.0, Illumina 1M.
I have looked in the recent nature and nature genetics papers where
76 - 27 % of the CNVs detected by a fosmid approach (Mapping and
sequencing of structural variation from eight human...genomes) were
verified depending on CNV size using affy SNP 6.0 (Integrated
detection and population-genetic analysis of SNPs and copy number
variation).
The sensiti…
div class="preformatted">Hello all,
I had an aha experience last night because of trying to count what
would be in Venn diagrams.
When calculating the expected overlaps...out the the 3-way overlap is the combinatorial
extension of the 2-way overlap formula.
#Let Array Size = AS
#Let List 1 Size = L1S
#Let List 2 Size = L2S
#Let List 3 Size = L3S
#Expected overlap of list 1 with list 2 = EO12 …
updated 14.3 years ago • Edwin Groot
Hi there! I am trying to perform a particular comparison after correcting for individual batch effects in DESeq2. The experiment involves the following samples:
condition individual individual_by_group side...differences between individuals due to inherent variability (as is known to be an issue with this experiment and as seen by PCA), I don't get very many DEGs. Therefore, I need to firs…
updated 5.6 years ago • elisa.t.zhang
pathview/>
<http://bioconductor.org/packages/gage/>
__Technical skills:__
Solid statistics training
Genetics/genomics data analysis (esp. GWAS, Whole Genome/Exome Studies), NGS data analysis, sequence analysis
R/Bioconductor...Enjoy computational/statistical method development, data analysis
Proven research/development experience, publication records
__Education:__
PhD…
updated 9.5 years ago • Luo Weijun
class="preformatted">
Anyone can help me in managing a dataframe?
I have data (.txt) like this (2 tables with one title, 4 columns and 2
rows per table):
group 1 num: 3
a b c d
1 2 3 4
6 7 8 9
group 2 num: 5
a b c d
4 6 8 10
2 12 6 14
And I want to combine...these tables in a da…
updated 13.5 years ago • Guest User
div class="preformatted">Dear BioC,
I’m running a metabolomics experiment using samples that were
collected from years 1999 to 2006. The study is unbalanced as the
diseased
samples were...taken in all years, the controls only in year 2000 and
2001.
The sample size per year varies from 8 to 29 per year.
For some metabolites the measured intensities are significantly
different
between
updated 19.3 years ago • E. Schwarz
I have a data set from the following Design of Experiment(DOE)
```
sample batch condition
FRT19A_se se FRT19A_Control_2
Hinfp_A_G_se se Hinfp_A_G_point_mutant
Hinfp_M2_11_se...W1118 vs Hinfp_M2_11
FRT19A vs W1118
```
Note: I have 4 samples, each has a replicate in batch(SE), another …
updated 6.7 years ago • aimin.at.work
Once again, we received excellent applications to serve on the Community Advisory Board (CAB) in 2021.
Nominations were voted upon by existing members of the CAB, and as a result of this process, we're pleased to welcome the
updated 4.9 years ago • Matthew Ritchie
in the deep mists of time a comment (?from Ben Bolstad?)
suggesting the use of a standard 'training set' of (say) 50 chips, to
which you would add your new chips one at a time and process.
All comments, thoughts, or experiences
div class="preformatted">Hi all,
i have a problem to control the node size of a graph using the
Rgraphviz.
i'm creating graphs using Rgraphviz in its new interface (using
"layoutGraph" and "renderGraph...and
this
also reults in a corrupted graph.
by the way, when i use the "dot" layout, the node size are OK. the
problem
is only with "neato".
another (probably related) problem i encountered …
covariates. We want to use a parametric model like DESeq2 to account for these. As with many OTU tables, it's extremely sparse. I find that there is a lot of variation in the size factors as well as an unusual looking dispersion...plot.
The OTU table is extremely sparse, I have filtered down the initial 15000 OTUs to only those present in more than 10% of samples. This...exp(sum(log(x[x >…
updated 9.5 years ago • jbatsx
Hey,
Is it possible to correct for both a location and batch effect using Limma?
I have 4 surfaces: PET, PE, Glass and Water,
5 locations: A, B, C, D ,E,
and 2 batches: 1, 2
enter OTU<-read.csv("filterotu.csv...lt;- as.matrix(tax)
group<-factor(targets$surface)
location<-factor(targets$location)
batch<-factor(targets$Batch)
dge&…
updated 5.3 years ago • Katherine
with a large data-set with multiple treatment time points and genotypes. To increase my sample size for one of the time points, I'd like to add in two samples that were collected and sequenced in a different run. Alignment...methods are also different (STAR vs Illumina DRAGEN).
I’ve merged the counts table (I had a different number of total genes so I removed non-shared genes) and then ran RUVr …
updated 2.9 years ago • Zainab
We have an RNA-seq experiment where multiple tumour regions per patient were sequenced (average 4/patient) and we are using DESeq2 to compare
seq data of 16 samples. I filtered the RNA-seq counts to obtain 18,841 genes and further performed batch correction and covariate adjustments on a vst transformed data using removebatcheffects().
Further using picksoftthreshold...was ![Cluster Dendrogram with power 26][2]
I recently read a [post][3] which suggested to use the table provided in WGCNA faq. The table suggests me to use the power …
updated 13 months ago • Vinesh
div class="preformatted">Does anyone know where to get R-Codes for Irizarry's Stochastic models
paper?
Thanks
Stephen.</div
updated 21.9 years ago • Stephen Nyangoma
and treatmentA but only one for treatmentB, as the second replicate failed quality control. The experiments spanned two batches, with the first replicate processed in batchX and the second in batchY. Each sample was derived...r
mdata <- data.frame(condition = c("ctrl", "ctrl", "treatmentA", "treatmentA", "treatmentB"),
batch = c("batchX", "batchY", "batchX", "batchY"…
updated 19 months ago • nhaus
read
annotation file
[1] "C:/Users/franklin.johnson.PW99-WEN/Desktop/Test/Yanmin's
Microarray Paper/Yanmin Microarray RAW/GPL11164.ndf"
(xys <- list.files(getwd(), pattern = ".xys", full.names = TRUE)[1])
[1] "C:/Users/franklin.johnson.PW99...WEN/Desktop/Test/Yanmin's
Microarray Paper/Yanmin Microarray RAW/GSM618107_14418002_532.xys"
But, doing this resulted in an error message:
seed &am…
updated 12.7 years ago • Guest User
div class="preformatted">Robert Gentleman and his team are pleased to announce a new training
course titled "Intermediate Bioconductor: Analyzing Microarray and
Sequencing Experiments" to be held in Seattle...to end users who want to learn more
about
Bioconductor tools for analyzing microarray and sequencing
experiments.
During lectures and hands-on labs, attendees will be presented
material …
updated 17.2 years ago • Patrick Aboyoun
starting point for my analysis.
My plan was to normalise the data using DESeq2 and then perform batch correction and then normalise again. But I'm not to sure at what step in the downstream analysis do I need to do the second...There might be two options here:
Option 1
1. Normalise bulk and pseudobulk individually (DESeq2)
2. Batch Correct (limma)
3. Continue with differential analysis until t…
updated 2.8 years ago • informatician
so I want to see if anyone has any advice that is more specific to my situation. I am working on a paper where I found that when the same sample is sequenced with two different sequencing pipelines (i.e. different sequencing...coefficients for the LFC between each pair of pipelines. The problem is that I have uneven sample sizes between A and B, and between each pipeline:
Pipeline 1: A = 3, B …
updated 2.7 years ago • reba.duncan
you to submit a manuscript for this session. All manuscripts
will
be peer-reviewed, and accepted papers will appear in both the bound
and
electronic online proceedings and will be indexed in PubMed. The
paper
submission
is in
bioinformatics,
computational biology, genomics, data-mining, and related areas.
Call
for papers: BCBGC-10, USA, July 2010
The
2010 International Conference on Bioinformatics, Computational
Biology,
Genomics and...pools and
on-site dining â all situated on 10 tropically landscaped acres.
Here, guests
can experience a full-service resort with discount hotel pricing in
Orlando.
We
invite…
updated 16.0 years ago • John Edward
is in
bioinformatics,
computational biology, genomics, data-mining, and related areas.
Call
for papers: BCBGC-10, USA, July 2010
The
2010 International Conference on Bioinformatics, Computational
Biology,
Genomics and...pools and
on-site dining â all situated on 10 tropically landscaped acres.
Here, guests
can experience a full-service resort with discount hotel pricing in
Orlando.
We
invite…
updated 15.8 years ago • John Edward
Hello all,
I have a question regarding batch effect correction with LIMMA. I have some proteomics data, and when I do my PCA plot I see that samples cluster by patient...each sample with a different treatment). For this reason I would like to include patient as a batch effect in my linear model (rather than use removebatcheffects because I then want to perform differential analysis...however w…
updated 6.1 years ago • sandra.murphy
of Evolution and
Ecology at
the University of Chicago. Fellow will lead research and author papers
relating to high density polymorphism analysis from RNA and genomic
DNA
hybridization data for evolutionary genomic...array designs
will be
generated and are available focusing on the model plant Arabidopsis
thaliana. Experience with R/Bioconductor, low level microarray
analysis,
array design, HMM,…
thing. At one place, it suggests that a correction vector is identified for a cell in the target batch which is an averaged correction vector from all MNN pairs of that cell with cells in the reference batch. The MNN pairs...help identify local variation in subpopulation of the target batch. But then the batch vector, the component of correction vector that is actually removed, is same for all ce…
updated 4.4 years ago • p.joshi
the
crlmmCopyNumber step in my R code.
I've set up a Phenotype file where I list my files and their Batch
groups. In my example case, group1 and group2
Name FileName Batch
A1 array-123.CEL group1
A2 array-223.CEL group1
A3 array.214.CEL...gr2-pheno.txt"
pd <- read.AnnotatedDataFrame(myPhenoFile, header=TRUE, row.names=1,
as.is=TRUE)
batch <- as.factor(p…
run DESeq2 on my data. Single tissue with multiple dosages. I now want R to combine the results tables (dosages vs no dose) into a single table which I will import into IPA for further analysis. I have been trying several ways...to make R do this for me but have not found the correct method yet.
Example table from one dosage:
baseMean log2FoldChange lfcSE stat pvalue padj
Apoa…
updated 5.4 years ago • minardsmitha
Hi,
I'm running the example code for Time Course RNAseq experiments (section 4.8.8), and I'm getting the following error 'Error in dimnames(x$table) <- value : attempt to set an attribute
updated 5.0 years ago • hakusen03
GenomicRanges"
> save(exons, utr5seg, utr3seg, trans, tInfo, t2g, # introns,
file="annotation-tables-forRNAseq.rda")
the resulting saved object size in my directory is 23mb
> print(object.size(introns),units="Mb")
22.9...object by running:
save(exons, utr5seg, utr3seg, trans, tInfo, t2g, introns,
file="annotation-tables-forRNAseq.rda")
the object size in my directory got up to …
Hi,
We have 2 groups of control samples that belong to 2 different batches, so I used DESeq2 with the desgin ~Batch+Condition for the test. We are pretty happy with the results. Then we want to visualize...to get the counts to plot but we still see very clear different pattern between the 2 batches. Is it expected and should we be worry about this? Here's the code I used the get the couns
```…
updated 17 months ago • tothuhien
manuscript for review.
Similar to your work, the proposed Online-RPA algorithm reads CEL
files in batches to update the hyperparameters of a probabilistic
probe-level model. This yields a fully scalable algorithm (linear...time
wrt. sample size) which systematically outperforms the standard RMA in
various benchmarking tests, is readily applicable to all Affymetrix
updated 13.2 years ago • Leo Lahti
<div class="preformatted">I've had several requests for references to published papers in the
biology
literature using the limma package. There have been three articles
appear
since June that I know of:
Golden...div class="preformatted">I've had several requests for references to published papers in the
biology
literature using the limma package. There have been three articles
appear
si…
updated 21.5 years ago • Gordon Smyth
matters.
I tried removeBatchEffect() and it works well. The example project I
tried
had four batches, one of which consisted of only single sample. How is
removeBatchEffects() able to deal with single sample batches when...ComBat
does not? Here is an example:
expr <- matrix( 10 + rnorm(10000*100), nc=100 )
batch <- paste0("Batch", rep( c(1, 2, 3, 4), c(33, 33, 33, 1) ) )
tissue…
updated 11.5 years ago • Adaikalavan Ramasamy
some power calculations for a dataset that consists of paired data. First, I calculated the effect size using Cohens D formula for paired data (found [here][1]). Later, I wanted to check how the power is affected when I use the effect...size calculated with the shrunken variance from the eBayes function (``fit$s2.post``) in LIMMA as recommended [here][2]. As expected...analysis, I also get larger…
updated 4.9 years ago • MoltenLight
Hi All,
I did DESeq2 on my set of samples and I got only two DE genes.
When I checked I found that my samples were collected at different time points and in PCA a prominent batch effect is shown.
So, I included a batch in my design
ddsHTSeq <- DESeqDataSetFromHTSeqCount(sampleTable = sampleTable,
directory = directory,
…
first time and I'm encountering some issues, one in particular is quite weird.
I've got a simple experiment, 3 conditions, 4 replicates each.
I've obtained peaks using MACS2 (-- broad function).
```r
SampleID Condition Replicate...that the number of reads per sample is extraordinarily high (at least two times the actual library size, which was around 60M SE). How is it possible?
…
updated 19 months ago • Marianna
div class="preformatted">Hello,
I have a question about which analysis to do in LIMMA. I did three
experiments (three biological replicates) each with one treatment
microcosm ("L") and one control microcosm ("D"). For each experiment...treatment and control microcosms at 5 time points
(0 hr, 2 hr, 6 hr, 12 hr, 24 hr). With 3 replicate experiments * (1
treatment + 1 control) * 5 time points, I …
Hi
deseq2 is good considering batches and I can see and remove them with a command
assay(vsd) <- limma::removeBatchEffect(assay(vsd), vsd$Batch)
and see with plot
updated 3.6 years ago • Syed Zaheer
I am working on RNA-Seq data. I'm using DESeq2 for my analysis. I have 20 samples from 3 batches. I am testing for 2 conditions, cond1 and cond2.
dds<-DESeqDataSetFromMatrix(countData=countTable3,colData=coldata...design = ~cond1\*cond2)
When i performed PCA, I could clearly see some batch effect. I read in the forum that adding batch to the design in DESeq removes the batch eff…
updated 9.7 years ago • AB
the samples are the ones with the highest amount of reads (and largely belonging to the same batch). Looking at the heatmaps it also is apparent that they cluster differently because of generally higher reads:
<img alt...src="https://i.imgur.com/C7S4O6L.png" style="height:475px; width:792px"/>
I thought the size factor normalization should take care of this? Removing the batch effect usin…
updated 7.5 years ago • ipso
exact details of the DESeq2 method in order to reimplement a simplified version of it in Stan for training purposes.
At the moment I am struggling to grasp how means for the negative binomial distribution of each gene...count_ K\_ij_ are computed.
## Information given in the paper from from Love, Huber, Anders (2010)
In the paper (https://genomebiology.biomedcentral.com/art…
updated 7.2 years ago • nikosbosse
Hello,
I'm using DESeq2 to model a multi-factorial experiment with two predictor variables: Genotype (binary) and Passage (integer):
# Make passage variable numeric
coldata_exp...test="LRT",reduced = ~ Genotype + Passage)
We would like to derive some measure of 'effect size' of the interaction which is that is comparable between genes;
or, how much does v1 affect gene expression …
<div class="preformatted">Dear BioC
I have a set of Affymetrix chips which have a clear "process day"
batch
effect. This effect is only partially removed by RMA, gcRMA, vsn or
invariantset "expresso" normalisation.
What would you...div class="preformatted">Dear BioC
I have a set of Affymetrix chips which have a clear "process day"
batch
effect. This effect is only partially removed by…
I have not seen asked yet and I am hoping for some feedback.
I have an RNAseq dataset in two batches with an imbalanced study design, and I had a large batch effect. I used combatseq to 'correct' for the batch effect.
PCA...from the original count matrix showed the large batch effect with PC1 ~90% of the variance. After combatseq, the batch effect is reduced (pc1 ~37%), but still appare…
I have 4
treatments at 4 time points, mostly in triplicate, spread
approximately evenly across 2 batches. Previously I have used ComBat
to reduce batch effects and then used Limma and AgiMicroRna to get DE
miRNAs. However...I read on the list somewhere that it is better to
add Batch as a factor to the model in Limma rather than try and remove
it.
### So this time I added Batch to my targets fi…
updated 14.6 years ago • Segal, Corrinne
now running ATAC-seq differential analysis by DiffBind with peaks from MACS2. I have 10 samples from batch 3 and 20 samples from batch 5. How could I eliminate batch effect and normalize them in DiffBind? Sorry, I'm quite new in this
Hi All,
I have a dataset which contains two batches. I wanted to remove that batch effect and further analyze the data (to perform differential analysis and clustering...Hi All,
I have a dataset which contains two batches. I wanted to remove that batch effect and further analyze the data (to perform differential analysis and clustering). I used two approaches:
1. giving the batch and the biolo…
updated 8.5 years ago • lirongrossmann
span style="font-size:13px; line-height:1.6">Dear Khaleel,</span>
The pattern should be written as "^<span style="background-color:rgba(255, 255, 255...font-size: 13px; line-height: 1.6;">https://support.bioconductor.org</a><span style="font-size:13px; line-height:1.6"> . Many thanks!</span...nbsp;
Best regards,
Julie
<span style="font-size:13px; line…
updated 9.8 years ago • Julie Zhu
For a manuscript revision we were asked to redo the data analysis of a standard RNAseq experiment (two conditions, triplicates, no transcriptional amplification,~50M reads/library) with a DESeq2 normalization...So far we only used the ERCC spike-in controls for addressing the technical performance of the experiment and removed the ERCC probe counts before feeding counts into DEseq2. The …
get some advice on controlling for random effects using DESeq2. For example, given simulated data:
<table border="0" cellpadding="0" cellspacing="0" style="width:144pt">
<tbody>
<tr>
<td>Treatment</td>
<td>Batch</td>
<td>Estrus</td>
</tr>
<tr>
<td>Control...Treated</td>
<td>3</td>
<td>1</td>
<…
updated 8.6 years ago • Dipro
Hello,
I have the following (certainly not ideal) RNA-seq experimental design:
- Batch 1 contains 40 samples with condition A + 12 samples with condition B
- Batch 2 contains 40 samples with condition C + the same...So, the 12 samples with condition B are technical replicates that have been profiled across the two batches.
I'm actually not interested in condition B; I need to compare th…
div class="preformatted">Hi Yan,
the idea was that the user constructs the batch array manually and
assigns it to the batch slot using the accessor method, e.g.
bt <- array(rep(1:2, each=5, dim=c(5,2,1))
batch(x...I(status),
pd[,-1L,drop=FALSE]),
intensityFiles=intensityFiles)
## if there is a batch column in the platelist file we want to
import it
if("Batch" %in…
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Thanks both for this useful information.
Comment: Reproducibility of code in various Bioconductor versions
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SNPlocs.Hsapiens.dbSNP155.GRCh38 is available for download from the same location as always. It has not changed since Bioc 3.20:
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