and interactions for a
2x3 factorial RNA-seq project we have been running (we have reasonable
replication: 7 biological replicates per treatment combination, i.e.
42 libraries in total).
>From our reading of the edgeR
Order by: Relevance
group.
arrayWeights allow me to get very interesting results but in
documentation it says you need replicates. Are they technical or/ and
biological replicates? I couldn't find clearly the information.
My second question is
834
9 YM_E3 YM 1094
10 YM_E4 YM 1313
11 YM_E5 YM 2643
```
I have 6 replicates for OM group and 5 replicates for YM group.
I am using a second factor which is numeric (taille).
I checked that colData
updated 6.1 years ago • emilie.derisoud
some RNA-seq time series data. I
have
four time points. The first and last time points have three
replicates,
while the middle two have two replicates. The following gives the
error I
get:
require(edgeR)
counts <-
read.csv
by different batches.
Say, we have multiple groups (A, B, and C) with 2 conditions (X, Y) and 3 replicates for each.
We'd like to list DEGs between condition X and Y in each group, and plan to do some posthoc analysis.
Group...conditions, and we came to know that group was prepared differently, say in batch 2 and 3.
Group-replicate-Condition-batch
A - 1 - X - batch1
A - 2 - X - batch1…
updated 4.9 years ago • gairoju
I have a simple loop of 2-color cDNA microarray experiments containing
6 individuals and 2 technical replicates for each. After batch and
printtip normalization I need the intensity values for each feature,
for each individual...design, not a reference design, I would like to
obtain intensity value estimates for all biological replicates. Is
there a way to get normalized intensities for all indiv…
updated 17.5 years ago • Lin Huffman
Array7 State2 Ref
Array8 Ref State2
Array1 and Array2 are technical replicates but dye swapped. Similarly
the other pairs of slides are dye swapped technical replicates.
The design matrix would...and below have been weighted zero.
Further analysis was done as mentioned in section 8.2 'Technical
Replication' and section 8.4 'Two Groups: Common Reference' of LIMMA
u…
updated 17.4 years ago • Arun Kommadath
we can help with our design. Currently, we are getting errors.
We have 18 RNA-Seq biological replicates (samples), each sample has
two columns of counts for each tag, one for the maternal allele and
one for the paternal...lt;-factor(c(rep(title, 18)))
parent1<-c("father", "mother") #parent labels for the first nine
replicates
parent2<-c("mother", "father") #parent labels for t…
gt; DBdata1
6 Samples, 5111 sites in matrix (7058 total):
ID Tissue Condition Replicate Caller Intervals
1 P359 SF Hotair 1 bed 4637
2 cP359 SF Unstim 1 bed 4313
3 P361 SF Hotair 1 bed 5100
4 cP361 SF Unstim...evaluation
> DBdata2
6 Samples, 5111 sites in matrix:
…
updated 6.6 years ago • rapmic
table>
I expected the log2fc to be -0.0892376619
I must say that this test is done without replicates, only one control sample vs its corresponding treament sample. Could this affect in some way??
When I perform the...same test with 3 controls and 3 treatments, used as replicates for the two conditions, the log2(fc) are correctly calculated.
\*\*The control and treatment samples shown here…
updated 9.8 years ago • Osvaldo
WT, 4d, 4e), each strain has uninfected samples(PBS) and infected samples, (KPn) and 2-3 biological replicates for each sample
I’ve corrected for background and normalized between arrays, using the quantile method, filtered...control probes and low expressing probes, and averaged replicate probes:
<pre>
targets<-readTargets("Targets.txt")
RawData<-read.maimages(…
updated 10.9 years ago • dsperley
Hi Aaron.
I have Time-series bulk data (with two biological replicates for each time) and now I wish to use it to annotate my single-cell data. My Single-cell data contains two samples, One...Your `vignette` is quite straight forward but can you tell me how I combine two biological replicates per time point into one column so that I have one column for each time point and use it for assigning la…
updated 3.7 years ago • rohitsatyam102
samples to Agilent chips. Our
experiment
is simply a comparison between two groups with 5 biological replicates
per group
(all 10 samples are biologically independent). From my reading, a
multi-dye-swap
and loop design both have...it could be extended more easily than
a loop
design in the future - i.e. add additional biological replicates at a
future date?
The idea behind the dye-swap is to get …
updated 16.8 years ago • Nathan.Watson-Haigh@csiro.au
t perform differential analysis.
The only thing I can think to do is set a threshold (i.e. all replicates must have > 10 gene counts) then say these are expressed. But I don’t think this is a very good way of doing it.
Do you
updated 4.1 years ago • AZ
My dataset contains mini-bulk samples (5 cells per sample). I have 6 replicates for each cell subset, meaning that I sorted 6 wells with 5 cells/well per subset. I've analyzed my data using the 'regular
updated 6.1 years ago • gmpjverstappen
and C are three patients
Would a paired t-test work better than one-way ANOVA here? Do I need
more replicates?
thanks for your help
Yogi
</div
updated 16.7 years ago • Yogi Sundaravadanam
Hi,
I have three group RNA-seq data, each of them have three replicates: MCF10A (normal), MCF7 (Breast cancer) and MCF7-TamR (Tam Resistant). I was wondering if there is a way to design a differential
updated 5.3 years ago • kf
millions of reads to the host but fewer reads of the parasite.
My library size of parasite by replicate is around 193,000. I have seen that "As a rule of thumb, we require that a gene have a count of at least 10–15", given my low
updated 6.3 years ago • vm.higareda
Hi ,
I'm trying to perform rrbs dme analysis using edgeR on 50 samples (5 replicates per timepoint /sex). It seems to be running forever (>8 hours) and not produce any output. Design matrix has 50 samples
updated 5.2 years ago • Archana
If only one out of five assays has replicate samples, is it possible to avoid specifying a sampleMap row for every column in every assay? Also, I notice assay...If only one out of five assays has replicate samples, is it possible to avoid specifying a sampleMap row for every column in every assay? Also, I notice assay columns
updated 4.7 years ago • Dario Strbenac
expressed genes? If so, how can I extract this subset? I have 5 groups in my PCA with multiple replicates and extracting the subset of genes that drive the PCA result will be very useful.
Also, is there a way to adjust the
analysis. I have been trying to
normalize 4 chips (two dye-swap experiments done in biological
replicates)
After doing backgroundCorrect(method="normexp") , one of the arrays
has all of its $G values at NaN.
This does not happen
updated 20.7 years ago • Palmer, Lance
pvalues in the result from glmQLFTest.
For example, I have 4 treatments A, B, C, D, each has 3 replicates, and I want to compare any treatment pairs, i.e.: A-B, A-C, A-D, B-C, B-D, C-D. I use a matrix, generated by "makeContrasts" to define
updated 6.9 years ago • zhang.jianhai
Hi,
I am trying to replicate the case studies at the end of the edgeR user guide to verify a workflow I’ve developed. Particularly I am interested
updated 5.7 years ago • ali.sajid.imami
a way to calculate within and between group variability
between two sample groups (with biological replicates) within DESeq ?
I went through DESeq manual, but couldn't find any reference. So is
the only way is to calculate
all,
I have a matrix of "A"/"P" calls. I want to filter for the probes that
are
present on all the replicates, for example
sample1_1 sample1_2 sample2_1 sample2_2
gene1 A P P
P
gene2 P P A
P
gene3 A P A
P
gene4 A A …
updated 14.7 years ago • Wendy Qiao
Hi
I have two replicates for two conditions ( resistant and sensitive ) at two time intervals for conducting a Differential Expression
Suppose that in my expression matrix I have 3 conditions: treatment A, treatment B, and control (2 replicates everywhere). Now my goal is to compare treatment A to control. My question is, should I do voom and further analysis
updated 6.2 years ago • chipolino
nbsp; factor="ER",condition="wt",replicate=2)
mESC <- dba.peakset(mESC, bamReads = "/home/tandrean/Desktop/mESC/3.sorted.bam",bamControl = NULL,
 ...nbsp; fac…
updated 8.9 years ago • fusion.slope
Dear Dr. Stark,
The following question has been asked before regarding error in dba.analyze step of diffBind when the contrast is set up for samples with no replicates. Obviously I should be comparing samples with multiple replicates but while I wait for more data from the sequencer it will be great if I could implement DiffBind for no replicates.
When I run __dba.analyze step__, I get the foll…
updated 10.7 years ago • danishm20
duplicateCorrelation
Dear Devin,
There are a couple of problems. Firstly, you've told us that your
replicates are 112 spots apart, but you haven't told limma this. So
the
software is assuming that the replicates are side-by-side...to check that duplicateCorrelation() is getting the right
input, the best way is to check that your replicates really are at the
spacing you think they are. Your data…
updated 20.1 years ago • Hua Weng
Hello,
I have RNA-seq data from 27 samples to analyse. I have 2 differents treatments (Compound1 and compound 2) + control (DMSO) and I have 3 times. I have 3 replicates for each combination.
I am trying to use DESeq2 to find the differentially expressed genes. First, may I double check...2 differents treatments (Compound1 and compound 2) + control (DMSO) and I have 3 times. I have 3 replicates…
updated 10.7 years ago • AurelieMLB
div class="preformatted">Hi,
I have 4 replicate slides. Within each slide, there are 3 replicate
spots for each gene. After doing the within Array normalization
updated 20.8 years ago • Yi Zou
and two time periods for a total of 10 different experimental conditions with 4-5 experimental replicates for each.
I'm using DESeq2 to analyze for DE of genes from RNAcounts.
There are really multiple comparisons...is a concatenation of two treatments, 3 surgeries and two time periods (this is 10 groups of 4-5 replicates each, because time period 2 is missing one surgery). …
updated 9.5 years ago • jshouse
towards a pooled mean so in principle it should work.
I used 7 genotypes, 2 treatments first with 3 replicates and then with
just 2 replicates. For contrasts I compared each genotype untreated
vs.
treated (ebfit p<0.01). On
Hello,
I have an RNA-seq dataset consisting of 16 species, each subjected to three experimental treatments, with three replicate individuals each. The species fall into three physiological categories. I would like to identify genes whose response...seq dataset consisting of 16 species, each subjected to three experimental treatments, with three replicate individuals each. The species fall into t…
updated 8.5 years ago • noah.reid
1:4], groups =
files$Treatment[1:4],
calibrator = "Control")
what to do bcz my samples have no replicate and groups consist of only
2
sample not 4 as in example file.
every sample have 26 features(13 replicate)
so how i perform
control) tested at 4 concentrations both with and without estrogen (E2). We had three biological replicates and three technical replicates per plate. We assigned samples labeled "control" to each chemical and assigned
updated 8.4 years ago • grashow
The figure above is derived from the code below
```r
viewPathway("E2F mediated regulation of DNA replication",
readable = TRUE,
foldChange = geneList)
```
[1]: /media/images/dd6fa916-fe9e-403f-b17f-0f53a2c9
updated 3.7 years ago • charlesgwellem
I am trying to conduct a `differential expression (DE) analysis` to identify enriched peptides in a `phip-seq` analysis using `edgeR`. However, as there are no replicates available, I am uncertain about how to determine the reliability of the ***BCV (square-root dispersion)*** utilized in...to identify enriched peptides in a `phip-seq` analysis using `edgeR`. However, as there are no replicates a…
updated 2.7 years ago • f_rahmdani
to 0 it's fine. But now i'm not sure if i should use a different cutoff instead of 0.
I have 3 replicates per sample
updated 6.7 years ago • anaQ
7 week , 9 week
* 4 different tissue: embryo, endosperm, mesocarp, pericarp
* 2 biological replicate for each
Regards
Yogesh
updated 9.2 years ago • nabiyogesh
preformatted">How does the vsn method compare to rma, in terms of bias and the
variance between replicates? Has anyone applied both methods to a
standard dataset and compared the results?
Thanks,
Tom Price
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Thomas S. Price
Hello,
I did plotcounts shows normalized counts for a single gene. two groups contains two sample which are not close together actually they are not replicates indeed, but the same library sequenced on two lanes. so I would appreciate let me know about such cases how should...single gene. two groups contains two sample which are not close together actually they are …
updated 7.2 years ago • lkianmehr
Hi all,
I analysed the list of DEGs in 10 tumour-normal pairs (without replicates), with edgeR. I used the paired design
<pre>
design = model.matrix(~Patient+Tissue)</pre>
Now, I would like to get the list
updated 7.5 years ago • takumima
Hi All,
I have 2 control and 2 treated replicates. I am running DESeq2 in order to identify differential bound regions form ChIP-seq samples. However, their are...Hi All,
I have 2 control and 2 treated replicates. I am running DESeq2 in order to identify differential bound regions form ChIP-seq samples. However, their are discrepancies
updated 9.6 years ago • p2016k
in the comparisons.
Is it OK to use DiffBind / csaw to compare these two ChIP seq samples (with replicates of course)?
Thanks
only raw read counts of RNA-seq. The design was quite weird. They applied the same procedure to the replicates but got sequenced in completely different platforms(Solid, Nextseq and Hiseq). If the procedures from fastq files
updated 7.6 years ago • krisd3v
Hello,
I would like to identify deferentially expressed genes.
I have 50 different individuals in three biological replicates (50 x 3=150) and they are not challenged for any condition (for e.g. control vs wild). I mean there is no treated vs non-treated...like to identify deferentially expressed genes.
I have 50 different individuals in three biological replicates (50 x 3=150) and they are no…
updated 9.9 years ago • myprogramming2016
Hello,
I have RNASeq data from 4 groups with 3 biological replicates.
The conditions are: 1) untreated, 2) treated with a drug, 3)infected with a virus, and 4) treated and infected.
I am looking
updated 6.4 years ago • sandraggava
Hello all,
I have an array with 8 groups and 4-time points (3 replicates in each), with the exception of 1 timepoint where the rats died. Reading about this missing group on Limma guideline
updated 5.0 years ago • ijvechetti
I wonder if anyone has experience doing an analysis with 3 biological replicates for the treatment but only 2 for the control? I am almost certain I screwed up one of my control samples during the
updated 9.2 years ago • hac141
I know this question has been asked before, but even reading through older posts I cannot replicate the LogFC output in R.
design <- cbind(Grp1=1,Grp2vs1=c(0,0,0,1,1,1))
data <- 1:6
fit <- lmFit(data, design)
fit <- eBayes
<div class="preformatted">Dear Guillaume,
The first approach (using duplicateCorrelation) is correct. The
second
approach accounts for technical variability, but fails to fully
account
for biological variability of the wt-mu contrast in the standard
errors of
the tests. The second approach therefore tends to be anti-
conservative,
and will usually lead to more apparent differential expre…
many significantly regulated genes (5 or
so), which is likely due to the small number of biological replicates
and the large diversity in the human population.
I also tried another approach, leaving the individual labels...why there is such a large discrepancy
between
the two analysis methods. Is this due to the way replication is
handled?
Could anybody comment on the validity of these two anal…
Hi,
I wanted to replicate the GO analysis done thru' (http://geneontology.org/), but using R/Bioconductor. For the 'original' GO analysis, I just...Hi,
I wanted to replicate the GO analysis done thru' (http://geneontology.org/), but using R/Bioconductor. For the 'original' GO analysis, I just copy...and click on 'Launch'. This resulted in a set of significant GO terms.
I am now trying to…
updated 5.3 years ago • Brian Smith
trtR/trtNR) and the sampling is done at 7 different time-points. I have different number of replicates: for trtR two replicates and for trtNR 5 replicates for each time-points (some time number of replicate is more).
I
updated 8.1 years ago • rahel14350
Hi,
I got an experimental design made of 3 replicates. Each replicate consists in a time course comparing the response of a cell line to a treatment "A" vs a placebo "B". Replicates...are not carried out on the same day, but within each replicate, treatment and placebo time course are carried out in parallel, usually starting from the cell line culture.
Experimental...series spline model.ma…
the
chromatin interaction differences between two conditions and I have
more than one technical replicates for each condition. However, I have
already the corrected matrices (with ICE and other methods) and I would
essentially
updated 9.5 years ago • lazaris
for an Illumina
gene expression data set (four lanes of paired end reads). I have two
biological replicates for seven time points. All packages that I am
aware of (bats, time course, edge) are designed for microarray data
analysis
updated 12.8 years ago • Sandra Rehan
Recent ...
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