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
Order by: Relevance
3 time points (6,24,48 hrs)
5 biological conditions (1 to 5)
2665 genes
2 biological replicates per condition expect for the last one that
has
6 replicates. (individuals 1 to 14)
In total I have 42 slides, thus the
updated 18.8 years ago • Ana Conesa
218
Three development stages 5 WEEK (5W), 7W, 9W.
Three tissue: Ca, Co, Pa
each with 2 biological replicate.
only 218\_5W\_Ca has one replicate:
My aim is to do pairwise comparison and to extract upregulated genes in Ca tissue
updated 8.6 years ago • nabiyogesh
term? One would duplicate the control condition so that the setup would look like so (ignoring replicates here):
<pre>
design(dds) <- ~Condition * Experimental_Condition</pre>
<table border="1" cellpadding="1" cellspacing="1" style...nbsp;
I also realize that this might mess with the dispersion estimates, as there is now a pseudo replicate.
Thanks,
-R
updated 8.0 years ago • rrcutler
Hi!
I am using MEDIPS.R package to analyze 45 methylated files. I have 45 files before pull down that i consider to be my Input_files for each 45 files after pull down considered to be my methylated files. I am running into issues when it come to create the MEDIPSData sets with them. I have 4 groups for which I create a vector containing replicates of each set:
Example;
bamfile_HN…
updated 6.6 years ago • rousselene.jones
Enter the body of text here
Hello everyone,
I have some questions about DESeq2 2-factor analysis. One of our ongoing project is about RNA-seq data from patient and control (2 genotypes) with or without stimulation(not stimulation, stimulation 1 and 2, 3 conditions in total), for each sample, we have different number of technical replicates, and we are very interested in interaction between gen…
L and B below) experiment, each of
which is
either present or absent.
I have 6 sets of biological replicates (includes equal numbers with
dye
reversals) of 5 of the 6 possible direct comparisons:
1)LB -> WB
2)WB -> WW
3)WW -> LW...effect per ?set of experiments", but has less (10
instead of
15) sets of experiments. B) gives more replicate sets (15 vs 10), but
within a
"set",…
updated 21.4 years ago • Michael Gates
Hi all,
I need help with the ballgown analysis (which I intent to use for my RNA-seq data with 3 replicates).
Right now, I am practising myself with this new tools by using the data provided in the article ___["Transcript...Hi all,
I need help with the ballgown analysis (which I intent to use for my RNA-seq data with 3 replicates).
Right now, I am practising myself with this new tools by usin…
I will just describe the experiment briefly
There are 22 samples, two samples are always a replicate. And the first two belong to the control group. I managed to calculate the mean value of each two replicates, logFC
nbsp;
I realize it is important to validate array findings wherever possible with technical replicates and more high-fidelity approaches like sequencing. Also it is vital to tailor your approach to the particular...the book or some blanket one-size-fits all approach. However, it is also important that results are replicable, and an important way of doing this would be to know to what e…
updated 10.5 years ago • maden.sean
for the peaks files and bam files containing read counts. There are two conditions, with two replicates for each:
SampleID Tissue Factor Condition Treatment...nbsp; Replicate bamReads ControlID&am…
Hello,
I am adapting limma to analyse colony-based fitness data in yeast (i.e. [https://en.wikipedia.org/wiki/Synthetic_genetic_array][1]).
For this, I am using `arrayWeights()` to calculate weights for each plate, and `duplicateCorrelation()` to take care of the technical replicates (where each yeast strain is grown multiple times next to each other).
After running the linear model usin…
updated 4.7 years ago • JohnTownsend
experimental design is a bit strange. I have 20 samples (expression at 5 time points, at 1 hr with 3 replicates, 2 hr with 4 replicates, 3 hr with 3 replicates, 6hr with 6 replicates and 10hr with 4 replicates).
I want to find the DEGs
updated 9.4 years ago • nashchem
analysis (classic approach: treatment vs control condition) in which library sizes of biological replicates of control thesis exceed of 100 times those of treatment condition. The software used, limma, is impaired in DEGs
updated 7.7 years ago • baus87
I have a file which I can modify
with sample names, gene names and Ct values where I don't have
replicates because I was using Fluidigm method for amplification.
How to do to use the function read.qPCR, how to configure
updated 11.5 years ago • Guest User
div class="preformatted">I am running limma 2.8 on a technical replicate dye-swap
design. Here is my design matrix:
(Intercept) as.factor(targets$time)24h as.factor(targets$time)4h
as.factor
using Agilent single channel data and found the `limma::avereps` function handy, since the number of replicate probes on the array vary per gene (locus). However, I would prefer to have **median** in stead of averages. Is there a possibility
updated 6.1 years ago • b.nota
you could clarify for me.
So in my chip-seq experiment, I have 2 conditions (2 biological replicates for each). Whenever I visualize the peaks in IGV or plot the MACS2 output bed scores in R, I see that overall, all counts
updated 10.7 years ago • mm2489
set have data from 8 different
developmental stages( A-H, each stage have at least 3-4 biological
replicates); The developmental stage are the same between the two; The
only difference between the two are the tissue source
updated 15.7 years ago • yan zhou
array and my experiment consists of 4 groups with treated/untreated data for 2 time points with replicates(3). I would like to use limma to find the differentially expressed genes between time points for treated and
updated 10.4 years ago • r.verstraten
Hello,
I am currently running "dep" package for my mass spectrometry data. Now I have the issue with generating heatmap
plot_heatmap(dep, type = "centered", kmeans = TRUE,
+ k = 6, col_limit = 4, show_row_names = FALSE,
+ indicate = c("condition", "replicate"),plot=TRUE)
Error in names(cols) <- var :
'names' attribute [7] must be the…
updated 5.6 years ago • nkvnambiar
nbsp; I am just interested in a comparison of drug vs placebo and consider cell lines are biological replicates. In this case, do I still need to put cells as a variable in the design as shown below? Thanks in advance.
design = ~ cell
updated 7.5 years ago • tombay82
I'm new to DESeq2 so I apologise if my question is a bit naive.
my dataset consists of 3 biological replicates of Control and treatment and I have performed Ribosome profiling and RNA Seq. I have a counts matrix which looks
updated 6.2 years ago • katerinadouka91
including 2 genotype, 2 treatment, 2 time point and 2 expression levels with three biological replicates (48 samples). When I treat each factor independently, I could find gene affacted by each factor separately. Since
updated 10.2 years ago • baibing7713661
V, Wrobel N, Gharbi K, Simpson GG, Owen-Hughes T, Blaxter M, Barton GJ. (2016) How many biological replicates are needed in an RNA-seq experiment and which differential expression tool should you use? RNA
<http://rnajournal.cshlp.org
to GLM. Say, I have A, B, C, D 4 treatments, and 1 control, each treatment (including control) has 3 replicates. All treatments and control are the same species. I want to compare A against B and A against control. I am hesitating
note that this gene is just "present/detected" once in the
Control,
but it is present in all the replicates of the treatment. In this
case: what
would be the right thing to do? To eliminate it from the analysis or
keep it
and
updated 14.8 years ago • avehna
I have three groups let's say C, L, and T, each with three replicates. I did comparison between C vs L, C vs T, and L vs T to find the Deferentially expressed genes in each compassion. I used
whether someone has written some R script to categorize
genes into different Go categories (e.g., replication, cell wall,...)
according to gene AffyID? I am working on ATH1 array. Or any hint/
quick
way to do it?
Thanks in advance
Fangxin
div class="preformatted">Dear All,
I have data without replicates. So, I have a single file for condition
and a single file for control. I know doing a differential analysis
will not
the results. I would like to appeal to the DESeq2 authors and maintainers to please keep the results replicable across versions, at least optionally by adding arguments to the relevant functions that allow the user to choose
updated 9.4 years ago • Peter Langfelder
tests. There is a gene of my interest. I want to dot testing between 2 samples/conditions (no replicates) to see if it is significant differentially expressed. Here is the normalized count for them:
 ...between cuffdiff and DESeq2), DESeq2 is always conservative to detect the signal. I know without replicates, all samples are considered as replicates of a…
updated 10.3 years ago • xfwang
Hi,
I’m trying to do some differential expression analysis which I believe that it should be trivial but I couldn’t find any reference for what I’m looking for. I’m pretty sure that the solution will be much shorter than the description below for what I’m looking for (sorry for that…):
I would like to find differentially expressed genes that indicate that a treatment A has a higher impact compa…
updated 7.9 years ago • Marina
years. There are six types of samples, a,b,c,d,e,f.
Each type has different number of biological replicates except type
f (no technical replicates). I am going to do pair wise comparisons
among these types.
For checking array
others, you need
to
test that tissue vs the others, but I'm sure you already know that.
If
you have replicates of each tissue, you can do pairwise comparisons
between the tissues, and choose transcripts which are consistently...up
in one vs all the others. If you don't have replicates, there's no
alternative really other than to treat the other 7 as a group.
Including lots of isoforms and using…
using cummerbund 2.0
but only some functions, and it works on the demo dataset.
My is data from replicates and density plots works - dens(), but not
the densrep() function, can this be a problem of the cuffdiff version?
Here is...RS-DBI driver: (error in statement: near ")": syntax error)
> densRep<-csDensity(genes(cuff),replicates=T)
Error in sqliteExecStatement(con, statement, …
updated 13.2 years ago • Guest User
expression analysis between matched paired
Normal
(N) and Tumor (Tumor) samples - 8 biological replicates (one tech
replicate
has been averaged after normalization). All samples are formatted in
one
matrix (M).
Signals have
updated 12.5 years ago • zhengyu jiang
Dear list,
I have a large collection of RNA-seq data (300 samples from different cells types, e.g. 2 samples from Basophils, 3 samples from cultured Mast cells etc; the number of replicates per cell type varies from 2 to 5). I would like to analyze the counts or the TPM data and find correlated RefSeq...types, e.g. 2 samples from Basophils, 3 samples from cult…
updated 7.9 years ago • Makis Motakis
Consider an experiment (e.g. proteomics) producing ratios. Our null hypothesis is that each ratio is one. In this particular example, I have a data table with n rows (peptides) and m columns (replicates). I would like to use limma to do a differential expression of each peptide versus a constant of one. This should be...ratio is one. In this particular example, I have a data table with n rows (pe…
datasets "qPCRraw"
it is
> mentioned that the 3 TagMan arrays "are 3 different samples with 2
> replicates each". Unfortunately, the only available information
> regarding the samples are sample names such as "sample1...sample5", and "sample6", making it difficult
to
> identify unequivocally which ones are replicates of the same sample.
> Having "phenoData" info…
cor$all.correlations from duplicateCorrelation) supports the
conclusion that the within-chip replicates are poorly correlated.
I am concerned that the numbers that are being handed to
duplicateCorrelation are incorrect...Ideally
I would like to be able to select a specific gene, calculate the
correlation between replicates myself and verify that this is the same
as I obtain from duplicateCorrela…
div class="preformatted">Hi all,
I have a set of 15 Affymetrix chips:
4 treatments, 2 technical replicates of 2 biological replicates for
each
treatment (one chips has been excluded, all the others are really good
quality
updated 18.0 years ago • Paolo Innocenti
Hello!
I am currently analyzing a RNA-Seq experiment where two cells lines were transfected with 10 different inserts that should decrease the level of 10 different targets that are present for sure in those cells. My goal is to detect the effect of the decrease of a given target at the transcriptomic level. The experiment has the following informations:
## __colData__
name cell vector…
updated 10.0 years ago • Radek
Hi,
I have been reading the previous post about nested and multi factor analysis with DESeq2 , as well as, the vignettes dealing with nested and multi factor analysis. However, I am still getting the "model matrix is not full rank" error.
Here are my experimental design and code that I have been trying to use.
The experiment was done in spruce with 6 clones and 4 treatments (CI, CW, MI, a…
updated 4.6 years ago • melissa.mageroy
Hi,
I'm looking at how different analyses of affy data perform on a sample
data
set of 2 conditions (untr vs. trt) with 3 biological reps (Ua, Ub, Uc
vs.
Ta, Tb, Tc). I've computed RMA and GCRMA expression measures as
standard and
so have 2 exprSets containing these values.
I've looked at fold changes and the treatment leads to many (1000-RMA,
1600 -
GCRMA) pairwise 2x changes (Ua-Ta, Ub-Tb, Uc…
Dear developers,
I am trying to find my way to plot VCF objects nicely, and I cannot run code from the help page (a section of "code not run" which may not have been tested in a while). Any suggestion? Thank you!
> library(VariantAnnotation)
> vcffile <- system.file("extdata", "chr22.vcf.gz", package="VariantAnnotation")
> vcf <- readVcf(vcffile, "hg19")
> ## default use …
updated 9.6 years ago • kevin.rue
An embedded and charset-unspecified text was scrubbed...
Name: not available
Url: https://stat.ethz.ch/pipermail/bioconductor/attachments/20070420/
45273f04/attachment.pl
updated 18.7 years ago • Artur Veloso
and then subsetted those genes from the TPM count matrix. I took the mean TPM across each replicate group and marked the gene as "expressed" if mean TPM >= 3. I was wondering if this approach seems reasonable, or if there
updated 3.2 years ago • nute11a
counts, normalized=TRUE) and (normTransform, f=log2, pc=1)?
2. Do I have to collapse the technical replicates using the (collapseReplicates) function before or after the deseq normalization?
3. I also want to filter miRNAs
updated 2.8 years ago • phmai1148
Hi,
I'm using deseq2 for a RNAseq experiment with 2 genotypes and 5 conditions (2 replicates for each combination of genotype and condition). When I use the deseq command to perform a comparison, I get different
of different genes with each other in a single biological condition (for which I have technical replicates). Transcript abundances were quantified using kallisto.
I'm a little confused with the output of tximport combined
updated 8.2 years ago • ctruntzer
Hi,
I would like to compare two groups (control,disease) which includes 3 replicates in each group. I followed the nature tuxedo protocol (HISAT,Stringtie and ballgown). In this method, There are ~700
updated 8.6 years ago • akilabioinfo
I'm trying to load in peaksets from a BED file (the summits output from macs2 callpeaks), and I'm running into an error
Here's what the first line of my BED file looks like:
chr1 4785666 4785667 BMDM-RNAPIIpS2-CTR-1-ChIPseq-GTACACCT_S9_L003_R1_001_peak_1 18.38304
And my DiffBind call us
ctr <- dba.peakset(NULL,
peaks="BMDM-RNAPIIpS2-CTR-1-ChIPseq-G…
I have three groups each have 4 replicates. The conditions for each group were same before preparing library and then sequencing. Now I have to analyse the
Trans 800
All experiments are perfomed with 3 biological replicates in each
group with Affy chips. I am
looking for differentially expressed genes in each groups as well as
dynamics
Hi again, sorry lots of questions at the moment,
I would like to replicate the following function from diffBind
<pre>
> dba.plotMA(tamoxifen, bXY=TRUE) </pre>
However I don't know how to retrieve
div class="preformatted">
Hi list,
I have five replicates comparing wt vs. mut.
But 3 slides came from one printing and the other two came from other
different printing (both
is needed) for processing a single channel. For example, I have very simple experiment, I have two replicates of WT and a treatment. I essentially have four columns which correspond to each array. I know which array is which
updated 9.4 years ago • sumneuron
years apart, different operators, etc...), we are seeing very significant differences in biological replicates as a measure of sequencer used. Perhaps the differences are solely the result of biological/technical variation
updated 7.7 years ago • JP Carter
<div class="preformatted">
Hello BioC,
I have a quick question about the proper way to normalize arrays
using gcrma. Right now I have a time series array, basically 10 groups
in total, each group has 2 replicates. The groups refer to time 0
(control), time 1,2,4,6,10,12...etc.
When I normalize these cel files, should I normalize them together...using gcrma. Right now I have a time s…
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