one potential issue. In the figure below:
Left is a scatter plot between 2 samples (biological replicates). Each point represents the read count at an **ATAC peak**. They are normalized by DESeq2 default normalization.
Right
Order by: Relevance
bootstrap values in my phylogenetic tree but instead of that I got the default number of bootstrap replicates in each node
updated 4.4 years ago • lanjarazakandrainy
the body of text here
hello, I combined the count number of three aspergillus strains with three replicates for each condition:
![enter image description here][1]
and the gene ontology for the reference strain N402 is as follow
Hi all,
I've been trying to perform a differential count analysis using Hi-C
data. I have two replicates for one condition, and only one for the
other comparison. The MA plot is not symmetric; there is a bias in one
direction
updated 11.7 years ago • Guest User
div class="preformatted">Hi,
I'm using Limma to find differentially expressed genes in a set of 2
replicate two-colour arrays, and I would like to know precisely how
lmFit takes into account the weights I gave to the spots
approaches to analyse differential reads counts \*per positions\*, between 2 conditions with 2 replicates each. I was thinking of using DESeq2, but modified in a way that the reads counts table would contain positions
updated 9.8 years ago • atisou
Dear Rory Stark,
Thanks for DiffBind package for analyzing ChIP-seq dataset that has multiple replicates. I encountered two issues when trying to add a derived consensus peak to an existing DBA object.
1. dba.overlap
updated 7.2 years ago • yuhongning2013
<div class="preformatted">hi friends
we are designing a microarray experiment, where there are two
different mouse strains (A,B)...
and one condition (Peptide - P and Saline - S). we expect the mouse
strains to express differentially even under normal (saline)
conditions...so we did not want to go for pooling the controls, to
have a common - pooled control... under this scenario...
which …
updated 20.7 years ago • vijayaraj nagarajan
three times (A, B, C). Each repeat is
measured at five different time points (T1...T5) in three replicates
(R1...R3):
A T1 R1
A T1 R2
A T1 R3
A T2 R1
...
C T5 R1
C T5 R2
C T5 R3
Thus, A T1 is matched with A T2, T3, T4 and T5, but not with the B
series
I am working on an RNA-seq dataset for differential expression: 4 environments, 4 biological replicates per environment. There are also 4 batches, but they are orthogonal to environments, so all environments are equally
updated 9.6 years ago • Ekarl2
Hi,
I am doing RNA-seq with 2 groups: treatment and control. For both of them, I have 2 replicates. I use limma-voom for this. But I am quite confused by the results I see in the toptable output. For example, I have these
am analysing co-IP mass spec data for two different animal conditions compared to control with three replicates each. The difficulty here is that the control is an empty bead without antibody, leading to rather expected missing
updated 7.9 years ago • alex.gos90
_As this concerns bioinformatics in general, I also posted [here](https://www.biostars.org/p/283215/)._
I am working on RNAseq data,
I made my count table using `` kallisto `` and then `` tximport `` to work with `` DESeq2 ``.
My genes are a set of cDNAs, (supposed to be corresponding to all the genes of my species), but the annotation is quite bad, when I align on these cDNAs I get 60% of map…
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
updated 5.7 years ago • bhakti.dwivedi
<div class="preformatted">
Dear Listers,
We have a case-control study and would like to use Agilent 4x44K
array. We only have three biological replicates. My questions are
1. Do we need to use technical dye-swap or we can use biological dye-
swap (budget issue)?
2. How does the...have a case-control study and would like to use Agilent 4x44K
array. We only have three biological repli…
updated 16.2 years ago • Jason Pear
pooled Control dataset
R1H1
R2H2
R3H3 =E
R4H4
the design matrix is such that I compared each total replicate in the
treatment i.e A, B, C, and D with E. Thus
A is compared with E
B with E
C with E
and D with E
Using BH method in LIMMA analysis
updated 17.5 years ago • yemi yomi
<div class="preformatted">I am using DESeq to detect genes that are differentially
expressed (DE). I am analyzing RNA-seq data from 6 samples, each of
which belong to different class with no biological replicates this
is
a poor experimental design as you noted in the DESeq vignette, but
this
is all I have.
What I am finding it to...am analyzing RNA-seq data from 6 samples, each of
which b…
0,0,0,0,0,0,1,1,1))
cont.matrix = makeContrasts(a-(b+c)/2, a-b, levels=design)</pre>
I'm trying to replicate my analysis with DESeq2. Here is some test data, and code to show I can extract DEG results between group a and b, b.
However
updated 8.2 years ago • chang02_23
div class="preformatted">Hi,
I have a technical replicates with dye-swap as:
Cy3 Cy5
-------------
wt1 mu1
mu1 wt1
wt2 mu2
mu2 wt2
wt3 mu3
mu3 wt3
wt4 mu4
mu4 wt4
designM <- c(1,-1,1,-1,1,-1,1,-1)
corfit
updated 19.6 years ago • Christelle Dantec
<div class="preformatted">Hi everybody
I'm using Affymetrix Genechip and I was wandering if it
is
reasonable to use a dataset whose genes belong to different analysis
of the
same experiment (a comparative analysis with three replicates). The
genes
belonging to all the analysis would compose the dataset to use for
further
analysis. I'd use the same bg...whose genes belong to dif…
updated 20.2 years ago • Marco Gentilini
containing different doses of a substance and also
have
multiple time points for each dose (with replicates). I am interested
in
classifying
the samples based on dose amount. I am experimenting with non-linear
techniques
Hello Everyone,
I'm running an RNA-Seq analysis for which I have 72 samples (mice), (6 replicates for each observed group). The main covariates are sex (MvsF) and cell type (A, B, C) from different tissues. Using voomWithQualityWeights
updated 5.8 years ago • pedrodcb
div class="preformatted">Hi all,
Just wondering if there was some way to replicate the expression-level
calls in
MAS5 here? I'm primarily interested in the calls made for each array:
is a
particular
updated 22.5 years ago • Paul Boutros
treatments (W,D), and 3 bioreps per strain/treatment
(1,2,3). There are 2 tech reps per biological replicate. Slide Cy3
Cy5
1 V3W H2W
2 H2W H1D
3 H2D H1W
4 V3D H2D
5 C1D H3D
6 C1W H3W
7 V2W V1D
8 V2D V1W
9 C3D V2D
10 C3W V2W
11 H1W V3W
12
updated 18.8 years ago • Heather de Glanville
Hi,
I have peak file for four different condition without replicate. I converted the text file to Bed file by taking column 2,3,4,8 and 5 which is chr, start, end, score and strand respectively
updated 10.4 years ago • Gyan Prakash Mishra
par. 2-way
anova)
for use on the AffyBatch class?
I have a strong batch effect between half my biol. replicates. Rather
than (continue) attempting to pull the two batches together with a
fancy
normalization, i thought i might
updated 19.3 years ago • k. brand
in order to calculate differential expression between different experimental conditions with two replicates for each. I understand deseq2 perform a normalization on the reads count in order to make the experiments comparable
updated 8.1 years ago • scamiolo
Dear all,
I am new using edgeR to compare two samples, each of which has three replicates. My code is as follows. However, I found that if ommiting `` coef=2 `` in the code `` qlf <- glmQLFTest(fit, coef=2) `` produces
updated 9.5 years ago • biolab
estimateGLMTagwiseDisp __(relative to a design matrix), even though there are no true biological replicates?
2. How do I calculate the prior degrees of freedom in this case?
Any help will be greatly appreciated
updated 10.9 years ago • Mauve
Hi
I have a count matrix (TPM) for my samples. I have 4 replicate for each sample. My samples are as follows :
wt0hr wt6hr wt24hr mut0hr mut6hr mut24hr
I have a TPM matrix
updated 8.2 years ago • tanyabioinfo
<div class="preformatted">Hi everybody
I'm using Affymetrix Genechip and I was wandering if it
is
reasonable to use a dataset whose genes belong to different analysis
of the
same experiment (a comparative analysis with three replicates). The
genes
belonging to all the analysis would compose the dataset to use for
further
analysis. I'd use the same bg...whose genes belong to dif…
updated 20.2 years ago • Marco Gentilini
2
Species B. tissue 2
I am using the design ~species + tissue (as I do not have enough replicates (~2) per condition to use an interaction model).
The contrasts available are "species A vs species B", "tissue 1 vs tissue
updated 5.6 years ago • Charlotte
the total number of peaks for MCF72 (43+47+57+885 = 1032) is different from the number of MCF7 2nd replicate listed in the output of the command dba(sampleSheet="tamoxifen.csv") on page 4, which is 1037 (so 5 peaks are missing
updated 11.1 years ago • Silvia
I am currently working on a time course data which has three genotypes and six timepoints with three replicates each. I used the vst function to normalize and then transform the raw data. Further, I performed weighted gene co
updated 8 months ago • Vishnu
I'm entirely new to limma/voom and the wider differential gene expression analysis field.
I have an experiment consisting of 20 patients, 7 time-points for each patient, and all 20 patients are undergoing the same biological process i.e. there is only 1 condition. There are no replicates for each time point.
I'm interested in determining which genes are differentially expressed as a functi…
updated 3.9 years ago • annaschumannuni
Hello,
I have some gene expression data for different tissue types with multiple replicates. My species has undergone a historical duplication event and and I am looking to compare the genome copies to...Hello,
I have some gene expression data for different tissue types with multiple replicates. My species has undergone a historical duplication event and and I am looking to compare the genome c…
updated 2.1 years ago • pl23
have a gene expression matrix with 3533 genes (rows) and
48 microarrays corresponding to 16 samples (replicates each). Out of
them 8 are from a sensitive and 8 from a tolerant cultivars. Samples
are taken at harvest and ripe and
updated 14.6 years ago • Clara Pons
using iGenomes UCSC genome
files
for hg19 genome. We have 2 Control and 3 KD samples( biological
replicates).
I have successfully passed the first step where in I prepapred the
annotation
file.
The second step which is "for
<div class="preformatted">Dear All,
I am PhD student, currently working on differential expression
analysis of
my smallRNA library deep sequencing data and trying to identify
differentially expressed miRNAs, using edgeR package. I have 24
different
samples with 2 biological replicates (48 libraries). I am performing
multiple group comparison using GLM method and also Anova-like test to
id…
updated 13.3 years ago • Danie
<div class="preformatted">Hi,
I have Affymetrix gene chip data from time course experiment with 2
different cell lines, 4 time points ("day0", "day7", "day14",
"day21"), 2 replicates at each time.
I want to "normalize" each probe at times "day7", "day14", "day21" on
its expression at time "day0"; following step...course experiment with 2
different cell lines, 4 time points ("day0", "day7",…
div class="preformatted">Hello,
I am trying to replicate results in a published paper, where they
performed a MAS5.0 normalization with the median normalized to 50 and
updated 15.1 years ago • Matthew Willmann
experiment: non-treated control, placebo-treated negative control, and treated cells. I have 3 replicates for each.
After running edgeR, and also looking at expression levels, I noticed that the negative control is not
updated 9.5 years ago • Peter
I'm using the CQN R package to normalize my data set where I currently have 5 cell types with 2 replicates each and analyzing DE peaks with edgeR.
1) Everything I've read so far suggests filtering before normalization
genes across the three species. now i have a table with the gene expression values for each replicates (\*3) in different treatments and log2FCby comparing to the mock and treatment of each responses.
Is there any
updated 8.2 years ago • laksharikrish
1% (which get published) are probably less likely to be real, but
these 1-3% effect size hits often replicate in external populations,
even
if the cpg has no effect on gene expression.
-Andrew
[[alternative HTML version deleted
updated 13.4 years ago • Andrew Jaffe
make
sense, as limma (eBayes) borrows information across all genes. There are about 50 biological replicates per group available.
Would you recommend to 'feed' limma only with the 700 genes of interest, or to perform the analysis
updated 11.1 years ago • Simone
Any help highly appreciated. Thanks!
Error message:
```
[1] "The bam files used:"
[1] "2 IP replicate(s)"
[1] "2 Input replicate(s)"
[1] "---------------------------------"
[1] "Peak calling result: "
[1] "2895 peaks detected on merged data."
[1] "Please check 'peak.bed/xls' under...FunDMDeep-m6A/DMDeepm6A_out/exomepeak_untreated"
[1] "1849 consistent peaks detected on every replicate…
updated 6.2 years ago • jovel_juan
T1, T2, T3) and UF has only one (T1). The coldata looks like this:
Sample Condition Time Replicate
AF_T0R2 CP 0 2
AF_T0R3 CP 0 3
AP_T0R1 CP 0 1
AF_T1R1 AF 1 1
AF_T1R2 AF 1 2
AF_T1R3 AF 1 3
AF_T2R1 AF 2 1
AF_T2R2 AF 2 2
AF_T2R3...timepoints to perform a time-course analysis using this coldata:
Sample Condition Time Replicate
AF_T0R2_2…
updated 5.4 years ago • gugpuccio
Hi everybody!
I'm starting to introduce myself into the world of differential affinity analysis, but I have a series of problems (please, forgive me my english):
I'm interested in doing a differential afinity analysis for multiple samples of a H3K27ac ChIP cancer's cells. I have many cell lines and also each sample was taken from different labs, so samples from a particular cell line …
updated 8.0 years ago • arcucamila
wt mu
> File2 mu wt
> File3 wt mu
> File4 mu wt
> *(four replicates of two groups (wt , mu) of which two replicates in
> each group is labeled by one color(red) the other two is labeled by
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...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 ge…
the
first 40 lines of header as well.
I should mention as well that with only two peaksets and no
replicates, you can not really perform a meaningful differential
analysis at the read count level!
Cheers-
Rory
________________________________...this info:
> tcf7data
2 Samples, 19 sites in matrix (1868 total):
ID Factor Condition Replicate Peak.caller Intervals
1 Treated Bcell …
Hi,
I have run DE analysis using different input files. One is with multiple conditions and another one is just pairwise comparison between treatment and control. I found that the p-value is kind of different. The input files are as below:
For multiple conditions, the input file is as below:
<pre>
condition replicate batch
Ctrl_A 1 1
T1_A 1 1
T…
updated 7.3 years ago • Louis Kok
for my
another data set which is four pairs of dye swap, four wild type
biological replicates and four mutant biological replicates. When I
run this function, I got Warning messages. I tried in two ways,
1) I only
updated 21.2 years ago • Ren Na
<div class="preformatted">Martin,
Google says: 'Your search - "subset.SummarizedExperiment" - did not
match any documents.'
So I offer the below for your consideration, along with a few examples
and a quick benchmark comparison with using the more explicit `[`
extraction operator.
subset.SummarizedExperiment<-function(x
,rowSubset=TRUE
…
updated 11.9 years ago • Malcolm Cook
the MID timepoint. In total we have little over 100 RNA-lib samples so theres quite a few biological replicates but no technical replicates. We have eliminated possible outliers based on PCA and heatmaps and are using RUVseq
updated 5.1 years ago • heikki.sarin
experimental design:
Genotype: RR, SS
Time: 0, 1, 7, 20 days
There are 6 biological replicates for each time point.
I would like to find a list of DEGs between genotypes taking into account time. For that I followed...pre>
> colData[sample(nrow(colData), 10), ]
# A tibble: 10 × 4
ID Genotype Time Replicate
<fctr> <fctr> <fct…
updated 8.5 years ago • ofonov
F, and P) grown under
three different agronomic conditions (L, M, and H). I have done 3
biological replicates. So 2 times x 3 varieties x 3 conditions x 3
replicates = 54.
Based upon the suggestions of some colleagues of mine, I
I have chip-seq data which I am analysing with Diffbind. I understood the "blocking factor" functionality of it can be used to remove confounding variables. In the Diffbind manual, the confounding factors used as examples are strings (e.g. cell line names, if the cells from those samples were "resistant" or not), but I would like to use numeric variables such as age or post-mortem delay (e.g. 80 …
<div class="preformatted">Hi to all!
I've to perform a time series analysis with timecourse package, but
I've got plotting problems and some doubt on experimental design.
I've 2 cell lines (first as parenthal, second as transfectant for a
specific gene), each with 2 biological replicates and 4 time points,
for a total of 16 samples.
Main goal is to find genes with different temporal behav…
updated 14.5 years ago • Andrea Grilli
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