1:9,1:3]
data.n <- data.abiotic[,rownames(design.n)]
colnames(design.n) <-c("Time","Replicate","Group")
design <- make.design.matrix(design.n)
design$groups.vector
# [1] "Group" "Group"
head(design.n)
# Time Replicate
Order by: Relevance
<div class="preformatted">Hi Heidi,
I am currently looking iwith interest at your package HTqPCR and I
have
the following question and suggestion.
The class "qPCRset" is really looking like a sort of "eSet" (defined
in
Biobase), just without "phenoData" or "assayData". Would it make sense
to get qPCRset to inherit from "eSet" ? This would likely facilitate
the
use of functionality in "Bio…
data(pairData)
pairCD <- new("pairedData", data = pairData[,1:4], pairData =
pairData[,5:8],replicates = c(1,1,2,2),groups = list(NDE = c(1,1,1,1),
DE =
c(1,1,2,2)))
As it indicated, The first four columns in these data are paired with
the
second...2, 7th and 8th samples (49, 68) as group 1, which is not
correct.
So I am not very clear with the replicates = c(1,1,2,2) and DE =
c(1,1,2,2).…
rather than 10,000,
thus
reducing my power;
- and not taking into account the technical replication we get
by
multiple spots on the array.
The limma manual has a section on Within-Array Replicate Spots. But
only mentions
this would be a
big help?
In general on what basis does one accept/reject arrays
from a pool of replicates! The hist() and boxplot()
shows clearly that all the arrays (replicates) do not
show the same "behaviour".
Here are the code
control1
6 control2
7 mutant1
8 mutant2
where I have 3 technical replicates and 2 biological replicates of my
control,
2 biolrep of mutant 1 and 2 biolrep of mutant 2. i.e.
As such how do I define
updated 17.7 years ago • Wendy Chen
<div class="preformatted">Dear Gordon:
I tried to use ebayes() method to pick differential expressed genes
for our
two color cDNA microarray data analysis. Our expreiment is designed to
anaylysis the influense of one chemical on cotton genes. It is a
Single-Sample Expreiment and two RNA sources are comapred deirectly on
3
biological replicates through time course. But we don't have complet…
updated 21.5 years ago • Hua Weng
I've seen voom normalization plots that have an S-shaped form, where the default lowess span in `` limma::voom `` appears to be substantially too large. For instance, appying `` limma::voom `` to the 48 replicate WT data from Schurch et al. (2016)
Schurch NJ, Schofield P, Gierliński M, Cole C, Sherstnev A, Singh V, Wrobel N, Gharbi K, Simpson GG, Owen-Hughe…
updated 9.8 years ago • Gregory Warnes
one can I choose in DEseq?
3.1 between two experimental conditions
3.2 working partially without replicates
3.3 working without sny replicates
Thanks a lot!
Best,
Liyue
-- output of sessionInfo():
> sessionInfo()
R version 3.0.2
updated 12.0 years ago • Guest User
rice. I have 2 genotypes (tolerant and sensitive) and 2 conditions (drought and well-watered) with 4 replications each. Basically, a 2x2 factorial experiment with 4 replications thus having 16 samples. I am working on 2 different
updated 7.8 years ago • tarun2
tissue samples, belonging to the same individual, at three different conditions, each in three replicates.
$df
sample group tissue
sample1-T-cond1 cond1 T
sample1-T-cond1 cond1 T
sample1-T-cond1 cond1 T
sample1-T-cond2 cond2...if this list is the same in the three different conditions.
I can't figure out how to manage the replicates and how t…
nbsp;
Hello: I am using DEseq2 for Small RNA-seq data. I have four replicates for control and two replicates for treated. I want to see differential expression of different kinds of loci (like
updated 9.3 years ago • mosharrofgeb
where I want to test for differential
expression in response to my applied treatment. As biological
replicates I
have two different genotypes of my clonal species, which were each
exposed
to treated and untreated conditions...this way in
general?
2) Does it also make sense in my case regarding the very low level of
biol.
replication (-> 2)?
Thanks a lot,
Lina
[[alternative HTML v…
updated 13.9 years ago • Lina Weber
genes that are thought to be essential for cell survival. It is a time course experiment with two replicates for each time points (4 time points) and we are interested to know if any of these shRNAs is consistently depleted...would appreciate if you could advise me on the best way to perform time course analysis with just 2 replicates on such a small shRNA-seq screen data ? And possibly…
class="preformatted">Dear Bioconductors,
I have some proteomics data for several tissues:
Heart x 3 replicates
Lung x 3 replicates
Each data set has a gene symbol and the number of peptides for that
gene (a
rough measure of protein
updated 15.9 years ago • Johnny H
the RUV normalisation? What is the most appropriate way to show clustering if there is such a clear replicate bias?
Thank you very much for your help! I really appreciate any feedback.
> samples <- read.table(file.path(dir...counts
summarizing length
> ddsTxi <- DESeqDataSetFromTximport(txi,colData = samples, design = ~ replicate + treatment)
using counts and …
that looks like a decay curve:
![Scatter plot shows time against "Number of UMIs per sample". Replicates are in different colours. Samples of the same replicate are connected by lines. Curves look like exponential decay...curves][1]
If we normalise by the sum of all UMIs for all time points in a replicate, that does a pretty good job normalising these curves (at least for two of the replicates,…
updated 21 months ago • i.sudbery
Dear community,
i would like to address an important question regarding an illumina microarray dataset, i'm currently re-analyzing. It's about the experimantal design of the dataset with GSE32091, which has also been publiced.
In detail, there are 3 different conditions (Irradiated, bystander, control) in 3 different time points( 4h, 8h, 26h) with 3 or 4 biological r…
updated 9.6 years ago • Konstantinos Yeles
Dear Michael,
I have a raw count dataset with three conditions (A,B,C) and each condition has 2-3 biological replicates. I calculated the normalized counts (not log2 transformed) in DESeq2, and for instance the following lists the normalized...I have a raw count dataset with three conditions (A,B,C) and each condition has 2-3 biological replicates. I calculated the normalized counts (not log2 tr…
updated 4.3 years ago • ting.chen.lrx
40 KB).
libfiles <- c("V010.mapped_tt.txt","V010.mapped_tt2.txt")
libnames <- c( "tt1","tt2")
replicates <- c("fGS_OSS","fGS_OSS")
aD <- readGeneric(files = libfiles, dir =
paste(datadir,"test/",sep=""), header = TRUE,
replicates = replicates
updated 14.2 years ago • jiayu wen
<div class="preformatted">Hello,
I have a problem with the design for an experiment that I'm
evaluating.
There are two parts to that problem.
The first part: we have two groups (A and B) after treatment, each in
three replicate, and two-color arrays have been created, with a
dye-swap for each replicate:
Cy3 Cy5
A1 B1
B1 A1
A2 B2
B2 A2
A3 B3
B3 A3
Here is how I'm doing it currentl…
updated 13.4 years ago • January Weiner
Formula design
We are struggling in understanding the correct design formula for my rnaseq analysis. We have 16 samples, 4 biological replicates with 2 different variables: if they are treated with a drug or not, and if they are stressed or not.
We want to know:
a...in understanding the correct design formula for my rnaseq analysis. We have 16 samples, 4 biological replicates with 2 differ…
updated 7.0 years ago • polyptwo
Hi,
I have been trying to install DESeq2 v1.35.0 to replicate some data I generated some time ago, but I cannot find this subversion.
BioCv15 has the v1.36, whereas BioCv14 the
updated 20 months ago • Espresso
a TPM count matrix. The columns are the samples wt0hr wt6hr wt24hr kd0hr kd6hr kd24 and have four replicates for each one of them.
Can some one help me with the correct R package to plot the PCA for samples when I have the TPM
updated 8.2 years ago • tanyabioinfo
NN report.parquet file. I assume there is an easy way to link the file names to their conditions and replicates ?
Cheers
Brett
updated 3 months ago • Phinney, Brett
with 3 pos/neg in each cell type.
I am either running all the samples in one dds with the design `replicate + group` or subsetting the object using:
```
dds_subset <- dds[, dds$group == "A_pos" | dds$group == "A_neg"]
dds_subset$group <- droplevels...dds_subset$group)
dds_subset$replicate
```
And then obtaining results with:
```
#No subsetting
A_res <- results(…
updated 3.6 years ago • Tom
Hi
I have a dataset which is pretty much IDENTICAL to the swirl dataset:
Experiment 1 - two replicate arrays with a dye swap:
TreatedCy5 vs UntreatedCy3
UntreatedCy5 vs TreatedCy3
Experiment 2 - two replicate arrays
Hi
I am analyzing ATAC-seq data for several embryonic replicates. An extract of my sample sheet looks as follows:
__Sample ID Tissue Replicate 
large? How much above the value of
1 is
> considered to be large?
>
> In my case, I have 2 replicates in each group.
Recommending a good cut-off threshold turned out to be rather
challenging. For two replicates, for
number of samples and coefficients to fit,
estimating dispersion by treating samples as replicates.
read the ?DESeq section on 'Experiments without replicates'</span>
I don't know what is the problem actually..
could
updated 9.4 years ago • ta_awwad
4 concentrations each, both in the presence of estrogen and without estrogen. There were 3 technical replicates and 3 biological replicates. The DESeqDataSetFromMatrix command looks like this (without interactions):
dds
updated 8.6 years ago • grashow
be
used for
further analysis work??
rownames(RG) <- RG$genes[,6] #I use that to sum over spot replicates
RGb = backgroundCorrect(RG, method="normexp", offset=50)
cy3.channel = RGb$R
cy3.channel.norm =normalizeBetweenArrays...weights)
log.ratio <- MA$M # this is the Ratio data with four spots per probe
#The median of the replicate probes:
Cy3.norm <-
apply(cy3.channel,2,fu…
updated 15.4 years ago • ashwin Vishnuvardhana
Dear all,
I am trying to run EBSeq on a RSEM count matrix containing 2 conditions with 3 replicates in each.
I ran EBSeq following the tuotrial and it worked well. However, I have 3 questions :
* How could I determine...Dear all,
I am trying to run EBSeq on a RSEM count matrix containing 2 conditions with 3 replicates in each.
I ran EBSeq following the tuotrial and …
updated 9.7 years ago • jean.keller
<div class="preformatted">Hi all,
I want to simulate counts for 1000 genes for 5 RNA-seq samples (with 3
biological replicates each), and I want to provide the dispersion
parameters myself.
Is there a package or code that can help me do this?
Thanks...Hi all,
I want to simulate counts for 1000 genes for 5 RNA-seq samples (with 3
biological replicates each), and I want to provide the disp…
updated 13.4 years ago • Alpesh Querer
1) and Power Archiver.
My downloaded archive has MD5 sum f777307d236b287d680e7a846b6553cd.
Can you replicate this error? Did the file go corrupt on the way?
Thanks and greetings
Johannes Hüsing
</div
Hi
I have column of gene expression of 208 (104X2) samples. I want to take mean of all replicates using R loop Can any one suggest me
w x y a b e
5 1 1 2 4 1
6 2 2 5 3 6
7 3 3 8 9 3
8 4 6 9 1 3
so for example i have have w x y a b e columns
I have several RNAseq datasets. I have one control and one treated sample and each sample have 3 replicates(6 datasets in total). I already got the count data for each gene using Kallisto. Can I use the count table from Kallisto
for most of the microarray packages...
When calculating the average differential expression for replicate
spots, do you take an averge of the log2(ratio)'s, or the log2 of the
average ratio? (they come up with different numbers
updated 20.0 years ago • michael watson IAH-C
0.492
The experiment consists of three treated groups each performed in
duplicate. However, the replicates have been split between two SMD
platforms/prints. For example, group A replicate 1 is on GPL3417 and
group A replicate
Dear all,
I have an experimental setup with one control sample and two knockdown samples done in two replicates. I made the two knockdown samples using two different siRNA construct so my problems is that i don't know how my deseq...nbsp;
I have an experimental setup with one control sample and two knockdown samples done in two replicates. I made the two knockdown samples using two …
updated 7.8 years ago • khhsource
<div class="preformatted">Hello Goutham-
You should not do any manipulation of the reads (including
normalization).
When you call dba.analyze the data will be normalized by the analysis
package(s) you choose (edgeR, DESeq, DESeq2) using the read counts
computed by dba.count.
There is an explanation of how the normalizaiton works for each
analysis
method near the end of the User Guide/Vign…
updated 12.2 years ago • Rory Stark
and time2(Off-A). I have more patients but for this example I am just showing two patients with two replicates and two time points. (Here P\*T\* are columns of my expression matrix).
Can you please suggest a DeSeq2 design matrix...for this?
2) Since the same patients were sequenced twice for both time points as technical replicates, does it make sense to combine the two repl…
<div class="preformatted">Dear Yannick,
Most clustering algorithms are invariant relative to linear
transformations, so you can cluster with your individual array data
without any transformation. It doesn't matter than you don't have a
common reference, except from the point of view of interpretting the
clustered patterns that you end up with.
(Personally I usually prefer to cluster on fi…
updated 18.4 years ago • Gordon Smyth
samples are a result of a more stochastic process and therefore I do not necessarily expect replicates to cluster together. The blue circles are control and green experimental samples.
<img alt="" src="https://i.imgur.com...branch. When I subset the data to only keep the controls and then remove the batch effect, the replicates do cluster together.
<pre>
condition batch
control …
updated 8.0 years ago • jaro.slamecka
Hi!
I am performing a differential expression analysis comparing cell lines responders to my treatment against cell lines not responders to the treatment (responders vs not resonders).
Here the sampleTable:
Name Cell_line condition
cell_line1_rep1 Cell_line_1 RESPONDERS
cell_line2_rep1 Cell_line_2 NOT_responders
cell_line3_rep1 Cell_line_3 NOT_responders
cel…
updated 4.8 years ago • dequattro.concetta
I have control and stimulated cell cultures for
individuals with and without disease (usually no replicates, but
sometimes up to 3 replicates).
Therefore I have two M vs A plots, control verses stimulus for the
disease group
<div class="preformatted">Hi,
My cDNA array have 2 duplicate for each spot.
I read and normalize my data set in limma.
I use the result MAList (MA) object in timecourse package.
But, I get a error:
> out1 <- mb.long(MA.2, times = 3, reps = size)
Time group assignments are set to default.
Replicate group assignments are set to default.
Erro em mb.1D(object, times, reps, pr…
updated 19.0 years ago • Marcelo Laia
cluster by genotype (as expected), but also by litter of mice. Typically, I have 3 biological replicates for each genotype, all collected on different days (i.e. from different litters). To deal with this, I have been using...vs. the "classic" exactTest method.
My problem arises in a new experiment where one of the KO replicates failed, but the matched WT was fine. The corresponding design matri…
updated 11.2 years ago • Michael Moore
Does someone knows if LIMMA supports this experimental design?
How do I have to consider (biological replicates, etc.) the
arrays?...I think they are indipendent? Is it right?
Do I have to calculate duplicate correlation among spot...replicates on
different arrays (I use arrays with only one spot per gene)?
How can I correct for the dye bias if I do not have any
updated 17.3 years ago • Erika Melissari
had the same question this morning - noticed a similar thing, while
re-running the analyses with no replicates, those with replicates work
OK.
Simon Anders has apparently been changing some stuff recently in his
functions
span style="background-color:rgb(249, 249, 249)">However, I am trying to run a data set with no replicates and it crashed when running calculateDiffMethDSS. It returns the error:</span>
<span style="background-color:rgb...color:rgb(249, 249, 249)">Do you have any ideas why? Could it be because that there are no replicates?</span>
<span style="background-color:…
updated 7.5 years ago • nilaycan
my friend to do some analysis on his affy data. He has a
simple 2x2 factorial experiment without any replication, i.e. only 4
chips. Because of this, I just perform MAS5, RMA and GCRMA on the raw
data with the default settings, and...a lot of changes even in the fold change
comparison. Is this discrepancy occured due to the lack of
replication?
Regards,
Fai
--
Yuk Fai Leung
Department of Molecul…
I have some questions after running DESeq2
As I can see in the data, some of the three replicates of one gene are all 0 reads count, why it still can be count log 2 fold change, or I misunderstood something
updated 3.8 years ago • YATING
I have RNASeq counts for one gene that was treated with 12 different drugs (with 3 replicates each).
I was wondering if anyone could please tell me which R package I should use to detect differential gene expression
of ~20 samples is required for robust WGCNA. I'm working with a set of 144 samples. These are two replicates for 72 different conditions. I wanted to make sure that using WGCNA in this case would be ok to identify coexpressed
updated 9.1 years ago • mh.manoj
<div class="preformatted">Hello,
I have microbiome data with no replicates, from different conditions.
I am
trying to transform the data using the DESeq method, as described in
McMurdie and...div class="preformatted">Hello,
I have microbiome data with no replicates, from different conditions.
I am
trying to transform the data using the DESeq method, as described in
McMurdie
updated 11.7 years ago • Sophie Josephine Weiss
The data matrix is small - 400 observations, for two conditions - cond1, cond2,cond2 (so only have replicate for cond2).
The plot has a distinct v shape:
http://imgur.com/a/2NDXw
Has anyone seen something similar?
Many thanks
updated 8.7 years ago • yul
Hello,
Is there a way to correct for within sample variability?? PCA plot show that some replicates within some samples have higher variability than others? Does this affect alot the DEG output? And is it possible
updated 7.6 years ago • sally_b86
nodes.
I used as an example the one in the Vignettes:
viewPathway("E2F mediated regulation of DNA replication", readable=TRUE, foldChange=geneList).
 
updated 7.5 years ago • juliethmurillo
<div class="preformatted">Hello Thomas-
This should work fine (using the same bam files as both ChIP and
control). I don't think I've actually tested this scenario, so if
there is a problem it would be a bug that would get fixed.
Cheers-
Rory
From: Thomas Nalpathamkalam <thomas.nalpathamkalam@sickkids.ca<mailto: thomas.nalpathamkalam@sickkids.ca="">>
Date: Fri, 26 Jul 201…
Recent ...
Replies
Answer: When to use edgeR or limma
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I updated the above answer today.
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James W. MacDonald
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I would use edgeR's quasi-likelihood model for any analysis with a smaller number of observations (like 3 vs 3 or similar), but if you have…
Answer: limpa-blank normalization and Spectronaut's PTM stoichiometry
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The short answer is that limpa reads standard feature-level intensities from Spectronaut or other quantifications tools. limpa is designed …
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mohammedtoufiq91
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@gordonsmyth Noted, thank you very much.
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