very few
significantly
differentially-expressed genes (highest B = 3.1).
I'm using three biological replicates, each hybridised to two dye-
swapped arrays
as technical replicates, on Compugen human 19k cDNA slides.
Is such a
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<div class="preformatted">
Hello,
I have three sequenced (Illumina) genomic libraries (L1,L2,L3) and
three biological replicates for each (A,B,C).
I'd like to compare those libraries, and find which are the most
similar (e.g. is "L1" more similar to "L2" or...<div class="preformatted">
Hello,
I have three sequenced (Illumina) genomic libraries (L1,L2,L3) and
three biological replica…
updated 12.1 years ago • Guest User
Hi Rory,
I am trying to analyze my chipseq data of H3K4me3 with 4 conditions and 2 replicates. I have only 1 replicate for input.
I think I create the sample sheet correctly and it works until some points but
updated 10.2 years ago • khani.sajjad
the data from the RNA-seq analysis of the 5 different groups (A, B, C, D and E) with 3 biological replicates each.
I would like to compare all my groups (B,C,D,E) to my control (A).
My question now is:
Is it better to compare the 2 specific...groups at the time (B vs A, C vs A...) using the input raw counts file containing all the groups and replicates (e.g. A1, A2, A2, B1...) using the DESe…
updated 6.5 years ago • sstankovic
data. It throws the error on 133aV2 chips
with
only 2 reps (not with 3) and with hu95 chips with 3 replicates.
The error msg is:
>Error in "names<-.default('*tmp*', value = c("100_g_at", "1000_at",
>"1001_at", : 'names' attribute [12625] must...siggenes code yet b/c I think this error has
been
discussed here - doesn't this happen when multiple replicate samples
have
identic…
Hi Michael,
First of all, I went through related questions posted earlier. Still, I couldn't figure out the exact answer to the question I am having.
My experiment is looking at the response to a virus that infects potato. I have conducted an RNAseq study to check the gene expression after 2 and 3 days post-infection . At each time point, I have 3 biological replicates (3 infected leaves ha…
updated 5.2 years ago • venura
RNA-seq data with four factors: Condition (WT and MT), CellLine (2 cell lines in each condition), Replicate (3 replicates in each cell line) and library (paired pull-down and control for a replicate): total 2\*2\*3\*2=24 samples (Table...WT and MT controlling CellLines. The issue is that cell lines are nested in conditions and replicates are nested in cell lines. How can I design the formula for …
updated 7.1 years ago • bioinfo
Hi here,
I have a question for comparing the interaction terms between multiple genotypes. I have three genotypes, two sequencing library types and different numbers of replicates for each sample type (see below sample description).
I'd like to compare the translational efficiency(i.e. Ribo/RNA...multiple genotypes. I have three genotypes, two sequencing library types and different numbers of r…
updated 9.0 years ago • szhen
that I have to analyze in order to find
differentially expressed genes. I have 10 biological replicates, and
each biological replicate has two technical replicates which appear as
dye swapped. So in total I have 20 arrays...limma to do my analysis. I know at the moment it is not possible
to treat duplicate spots, technical replicates and biological
replicates, but I though if I use the duplicateC…
<div class="preformatted">At 05:48 AM 7/08/2004, Richard Friedman wrote:
>Gordon,
>
> I now believe that I understand your answer. In order to do
> adjust for both multiple comparisons and
>multiple tests I use classifyTestsF() with method="fdr". If I
understand
>the documentation correctly, the fdr part
>refers to the multiple test …
experimenter how the samples were harvested and process and
CONFIRM that they are true biological replicates. It's amazing how
many
lab plant biologists see pooled samples from a bulk of plants grown at
the same time as biological...replicates when they are clearly not.
Looking at the RNA-deg plot (and sample labels) I guess they could be
epidermis cells or...to the
> other conditions lea…
updated 20.0 years ago • Matthew Hannah
class="preformatted">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 da…
Hi,
I used DiffBind for a collaborator who noticed that, contrary to his expectations, a particular region (which overlaps highly significant (pvalue << 0.001) peaks from MACS2 in each replicate of condition Y) got a very low FDR when compared to condition X (in which there are no peaks from any of the 4 replicates). Could you please help me to figure out if there's anything wrong …
updated 8.7 years ago • Silvia
<div class="preformatted">Dear Erika,
limma doesn't explicitly handle irregular replicates. (In my lab, we
haven't had to work with any of the new generation of Agilent arrays
yet,
so haven't had to solve the issues with them.)
Your best bet may be to simply average over the replicates for each
probe,
after normalisation, and before using lmFit(). This is not hard, but
requires some pro…
updated 17.6 years ago • Gordon Smyth
Hi everyone,
I have 16 rna seq samples (not replicates) and I want to compare 8 vs 8 which are paired matched.
Are there any adjustments when using Deseq I can make for the
updated 8.2 years ago • lirongrossmann
Hello,
I'm new to DiffBind and have 3 tissues with 2 replicates each. I have been able to generate plots with contrast 1-3 to compare each pair. I'd like to plot a Venn diagram of the
updated 5.1 years ago • Divya
For each sample (and replicate), do I have to convert zero read counts to ones (pseudo counts) while running deseq2?
<span style="line-height:1.6">I assume
updated 11.1 years ago • Prasad Siddavatam
de novo assembled transcriptome) or the tpm/fpkm values should be used for this comparison. no replicates are available for any of the species
updated 7.4 years ago • mailmashidur
package for Bioconductor has a function to
plot
and calculate the Pearson correlation for biological replicates?
TIA
[[alternative HTML version deleted]]
</div
class="preformatted">Dear all,
Is there a statistical test to compare standard deviations (within
replicate samples) in expression values of raw data and normalized
data?
Thanks in advance
</div
updated 13.4 years ago • Ali Mohammadian
to do summary statistics on individual
CEL files?! How does one accept or reject a CEL file
(from replicates) for further study?
Thanks,
Hrishi</div
updated 20.8 years ago • hrishikesh deshmukh
populations. There are more than 200 cell types in there (with raw data coming from 2-3 biological replicates that are accessible in [this ](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE15907)and [this ](https://www.ncbi.nlm.nih.gov...Would limma work in my case? An important factor to consider here may be the numbers of biological replicates per cell type (some samples have 2 and most o…
updated 7.6 years ago • atakanekiz
they found
differently expressed genes from these two separate chips, they have a
sample set (with 2 replicates each) on U133A and the same sample set
(also with 2 replicates each) on U133B.
I would like to maximise the available
updated 13.3 years ago • Zack Will
or to analyze each group separately. We have two experimental
groups and one control with multiple replicates for each from
different
animals. The three conditions were run at the same time for each
replicate
to minimize
updated 22.9 years ago • Gordon Barr
<div class="preformatted">Hi,
I just came across the latest update on the vignette of "DESeq". I
really like the new additions on visualizations particularly the
visualization of expression data from genes. In my rna-seq experiment
I have two conditions/treatments and three biological replication per
treatment. I did the differential expression analysis and variance
stabilized data using "D…
updated 14.6 years ago • Reddy.Thumma@csiro.au
approaches to ChIP-seq analysis (relying on external software
such as MACS) do not make analysis of replicates easy. I've seen
people looking for peaks and then compare the common/differential
intervals between replicates
setUQ <- betweenLaneNormalization(set, which="upper")
genes <- rownames(counts)
replicates <- makeGroups(control) # control is a column of sample_info and therefore information from the SeqExpressionSet...setRUVs9 <- RUVs(setUQ, genes, k = 9, replicates)
plotRLE(setRUVs9)
Thanks a lot in advance.
Felicitas
data sets where down regulated genes will still be expressed at lower level. The variation between replicates is also high, and so, we have at least ten replicates for each condition. Even with all these limitations, I am able
updated 10.3 years ago • sunil.mangalam
experiments is based on gene expression of a single tissue with contrasts between 3 treatments of 3 replicates. Each set of replicates was sampled from the same population and prepared and sequenced concurrently.
We have
updated 6.7 years ago • Jack.Hearn
am analyzing data of qPCR plates in which each well correponds to a
miRNA.
The system does not have replicates within the same plate.
the data consistes in 3 types of cells: I have 3 replicates for cell
type
one; 2 replicates for...cell type 2 and only one sampled cell type 3.
The data of each cell type and each replicate is in a separate file
where
the data has 5 columns
miRNA ID Target or Endo…
Hello,
I've done some differential expression analysis with 3 main groups (3 or 4 biological replicates for each group, 11 total samples). When comparing any two of the groups, there are a number of genes that are statistically...Hello,
I've done some differential expression analysis with 3 main groups (3 or 4 biological replicates for each group, 11 total samples). When comparing any two o…
updated 6.3 years ago • hsbio
<div class="preformatted">
Dear All,
Now I'm using limma to do microarray analysis.
In limma User's Guide (ver. 22 October 2008), Chapter 9, there is only
one case for "Separate Channel Analysis of Two-Color Data".
My question is, if there is duplication spots within each array (e.g.
3 spots/gene) , how to use duplicateCorrelation() to correct within-
array replicate spots in this case?
…
updated 17.0 years ago • Kun Zhang
I am performing an analysis for diff. expression on insects. The insects are treated with two doses of an insecticide (let's call them "low" and "high").
The setting of the experiment is the following:
- 5 x Control (biological replicates, several individuals pooled per sample)
- 5 x exposed to low dosage (biological replicates, several individuals pooled per sample)
- 5 x exposed to h…
updated 6.1 years ago • michael
<div class="preformatted">Hi everybody,
I have to come back to the issue of replicates probes in the Agilent 4
x 44K.
Reading for example the answer of Gordon Smith
http://article.gmane.org/gmane.science.biology.informatics.conductor/1
3846/match=agilent+probe+replicates
I completely agree with him to treat the replicated probes, doing the
analysis to select the differentially expressed..…
support site here and Gordon explained [several threads][1] that this happened if data doesn't have replicate. I am not quite sure how to proceed with my analysis now. How can I know data have replicates or not? If there is not replicate
updated 6.5 years ago • Jurat Shahidin
Hi!
I'm trying to replicate the example given in the plotBed example in the Suhi vignette, the one using the circles. However the Sushi...Hi!
I'm trying to replicate the example given in the plotBed example in the Suhi vignette, the one using the circles. However the Sushi\_ChIPSeq
updated 9.8 years ago • Till
class="preformatted">Dear List,
I am attempting to measure the reproducibility of two biological
replicate
RNA seq Solexa reads. Are there any Bioconductor packages that can
handle
this?
TIA
[[alternative HTML version deleted
updated 15.9 years ago • Pete Shepard
div class="preformatted">Hello everyone,
I have 5 variables, denoted as A to E, each with several replicates.
Is
there a reasonable statistical test to check whether (A-B)/(A-C) is
equal to
D/E?
Thanks for your help,
-Weibo
[[alternative
updated 15.4 years ago • xie weibo
points (1hr, 8hrs, 24hrs), including the control condition.
Each timepoint & condition have 4 replicates.
I was reading the limma user's guide but I am unsure about the following:
- is the approach using splines (9.6.2) possible...how to select the correct number of dfs?
- Should I use `duplicateCorrelation` since the same replicates were measured throught time?
- Is the following …
getting bit confused due to many interlinked options. If the metadata (information of case, control, replicates, bam files, peaks files, and format) are mentioned in a csv file and the analysis is run straight away with the command...1. Does DiffBind make two consensus peak sets (one for each: case and control condition) using the replicates within each condition or does it make one consensus pea…
updated 2.8 years ago • tahir.msajid
of transcripts at different subcellular fractions in *E. coli*. I collected three biological replicates, and for each replicate, I have the following samples:
SampleA: total RNA.
SampleB: RNA isolated from specific fractions
the experiment), DE comparisons have been performed between 2 samples (treatment vs control) with 3 replicates each (i.e.: controls_locality1 vs treatments_localitity1; controls_locality2 vs treatments_localitity2...groups of the same locality, it’s hard for me to understand how a gene with zero values in its six replicates is highly up-regulated (i.e: logFC=8.3) in locality1.
Thank you very m…
updated 4.7 years ago • Laura
two
slides represent the same original RNA sample and therefore
(partially)
represent a technical replicate?
It appears that limma lumps all of the slides together regardless of
which slides are supposed to be paired with...to me
that these pairs of slides must be considered independently from other
biological dye-swap replicates. Can anyone shed some light on how
limma handles this?
Thanks in…
Or
perhaps you might be able to
align the different arrays after averaging over the within-array
replicates. There aren't any
functions available to do this for you automatically.
Gordon
> Date: Wed, 25 May 2005 19:20:24 -0400...global) if
arrays have
> different layout(different location and different number technical
replicates
> (number of spots of a gene on an array))?…
updated 20.6 years ago • Gordon Smyth
Hi,
I have two questions about my RNA-Seq datasets that I have analyzed using Deseq2. I have used PCA plots for exploratory purposes. Out of the two groups (each group has 3 biological replicates) compared, samples of one group are spread apart on the plot and its really hard to decide which of the samples should be removed as outlier to proceed to differential expression analysis.&…
updated 9.2 years ago • Mnoon
<div class="preformatted">Dear List,
I would like to use EBarrays to analyse 24 MAs without replicates. I
have 12 samples taken at one time point, and 12 taken at other time
point. I want to find the genes differentially express at one time
point vs. the other.
I have chosen EBarrays because I don't have replicates. Until the
fitting of the model (emfit) it seems to work. However, when I w…
we have 9 samples in each group (three cell line in biological triplicates) and consider them as the replicate of each other. Then we can simply compare 9 vs 9 samples. However in this way we don't consider biological heterogeneity...between cell lines.
2.we have three cell line and three replicates for each and we want to do group comparison like the following
((control - cell line1) …
updated 7.7 years ago • amir_b_e
Reproducibility
(Statistics::Reproducibility - Reproducibility measurement between
multiple replicate experiments) in perl?
Thanks,
Nu
[[alternative HTML version deleted]]
</div
updated 11.9 years ago • nooshin
microarray data.
There are 8 samples (from 3 groups)
1. 4135447095_A& 4135447095_B the replicates (patient with rupture
'R')
2. 4135447095_C, 4135447095_D are replicates (control 1 - 'C')
3. 4135447095_E& 4135447095_F...are replicates (control 2 - 'C')
4. 4135447095_G& 4135447095_H are replicates( patient without rupture
'W')
I have used following code
updated 16.4 years ago • Md.Mamunur Rashid
TRUE,minOverlap = 1)</em></pre>
I had a surprisingly low correlation (< 0.2) between biological replicates. Here is an example for K4Me1, showing the correlation heatmap reported by DiffBind when creating the dba object...D0K4Me1\_1 and D0K4Me1\_2 are replicates for the time point D0, while D6K4Me1\_1 and D6K4Me1\_2 are replicates for the time point D6).
<img alt="" src="h…
updated 10.6 years ago • Pierre-François Roux
from WT mice as well (to ensure the FP didn't alter global expression). Thus, there are 3 paired replicates of sorted cells and unsorted (bulk cell prep) for the mutant FP expressing mice, and 3 replicates of unsorted (bulk...WT Rep 3 Unsorted..........F..........Unsorted
As expected, the unsorted WT and FP-expressing replicates are virtually indistinguishable in the rlog PCA, while the sorted…
updated 6.0 years ago • SeqGoblin3
iPSC lines were derived from the same starting material, so they can be considered to be biological replicates of each other.
The main question I am trying to answer is what genes are significantly up/down regulated for a given...claimed, however, that this was an inappropriate use of `DESeq2` since I do not have the right replicate structure. He claimed that I needed biological replicates th…
updated 6.6 years ago • wunderl
process between control RNA and treatment RNA.
- The data comprises n*m slides (*n* biological replicates and *m*
technical replicates for each biological replicate).
- The control label dye (cy5) treatment label dye (cy3) remain
Hello,
I have 5 treatments with 3 biological replicates and 2 technical replicates for each one. My design looks like:
1. DMEM (Basal condition)
2. Vehicle (Basal condition...After collapsing the technical reps my `sampleTable` looks like:
```
condition Replicates sex
Drug 1 male
DMEM 1 male
drug_insult 1 male
Insult 1 male
vehiculo 1 male
Drug 2 fem…
Hi,
I have RNA seq data with the samples defined as follows:
**ID level stability type**
A1 med unstable exp
A2 med unstable exp
A3 med unstable exp
B1 med stable exp
B2 med stable exp
B3 med stable exp
C1 low stable exp
C2 low …
updated 6.4 years ago • HD
gt;
> Thank you very much for your answer. I'm glad the function works
with
> biological replicates. Concerning the other points, you said that
one
> group is more consistent than the other one. When this appears...allow me to get very interesting results but in
>>> documentation it says you need replicates. Are they technical or/
and
>>&…
updated 13.4 years ago • Gordon Smyth
div class="preformatted">Hi,
I have RNA-seq count data for 3 genotypes(3 replicates each) for the
same
conditions. Is there a way to find most variable genes among all
three?
Thanks,
Shreyartha
[[alternative
updated 14.8 years ago • Shreyartha Mukherjee
I am running a DE analysis on edgeR. I have 8 biological replicates, in groups of 2 (1 normal and 1 diseased)
What I want to do is keep those genes, for which the cpm is above 4 in at least...I am running a DE analysis on edgeR. I have 8 biological replicates, in groups of 2 (1 normal and 1 diseased)
What I want to do is keep those genes, for which the cpm is above 4 in at least 4
Is performing a moderated t-test for differential expression appropriate with one group having no replicates?
 
updated 7.5 years ago • mrupji
Dear all,
Newbie.
I have an expression matrix with ~760 genes, 40 samples and each
sample has 4 replicates (=160 columns). May I use
Matrix= impute.knn (My.matrix)
Or should I detremine some parameters? Thanks in advance.
</div
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