I actually need to download pdfs through R code. The thing which I
want
to do is that, search for a paper in pubmed, which is possible by
using
GetPubMed function in the package "NCBI2R?".
GetPubMed(searchterm, file = "", download...all hits, although
if
I go to the pubmed, I can download it.
So, the problem is not that, for each paper I have to download the
pdfs
(which are available if I go to…
Order by: Relevance
AAT Level 4](https://www.fctraining.org/aat-level-4.php), you can trust that Future Connect Training will offer top-notch instruction tailored to your level of expertise.
Furthermore, Future Connect Training's flexibility...valuable for working professionals looking to upskill or change careers.
Lastly, Future Connect Training's track record of success speaks volumes. Many of their students…
updated 2.3 years ago • codymax
There seems to be some problem with OSAT that doesn't return the same size of data that was used for input:
``` r
library("OSAT")
data(survey, package = "MASS")
VoI <- c("Sex", "Smoke", "Age")
n_batch <- 3
iterations <...There seems to be some problem with OSAT that doesn't return the same size of data that was used for input:
``` r
library("OSAT")
data(survey, pa…
updated 4.7 years ago • Lluís Revilla Sancho
div class="preformatted">Hello,
having conducted 2 microarray experiments of the same cell line, and
on
the same affy chip in two seperate facilities we were given CEL files
of
different...size (13 & 30 MB). Can I compare them? Is there a way to
normalize them together?
</div
updated 18.2 years ago • apolyzos@bioacademy.gr
Hi,
I am using EdgeR for differential expression. The experiment includes five individuals who receive the vaccine in 4 different time points (pre, 2hour post, 24hour post, 14-day...in a way that i get results. i did `PlotMD` as you saw in the [image][1] sample 5-8 show separate batch in contrast to others. I intend to make the identification of DE genes using a log2 fold change and likelihoo…
in the same contrast. I've read the edgeR and limma user guides, the team's [Law et al 2018][1] paper, and many posts on bioc and biostars and haven't found this analysis question answered.
**Experiment Details** representative...6),
Temperature = rep(c("Low", "Low", "Low", "Low", "High", "High", "High", "High"), times = 3),
Batch = c(1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2,…
updated 9 months ago • Elizabeth
Hi,
My QIIME biom output only has OTU and taxa tables (see below). How can I add a sample\_table to my phyloseq object?
thanks!
<span style="line-height:1.6">> myboject..._biom(biomfile, parseFunction = parse\_taxonomy\_greengenes)</span>
> myobject
phyloseq-class experiment-level object
otu\_table() OTU Table: …
updated 10.9 years ago • Brian Smith
to simulate RNA-seq data using pilot data, to test the power of different sample sizes in an experiment with two treatments.
However, I am confused about how to input the parameters from my pilot data. Disclaimer...I am a biologist not a statistician. I have tried to understand the methods section of the DEseq2 paper, but unfortunately I still don't follow how to do this.
For example, fro…
updated 18 months ago • li.d.peck
sets in package golubEsets:
golubMerge (golubMerge.rda)
Combined Test and Training Sets from the Golub
Paper
golubTest (golubTest.rda)
Test Set Data from the Golub Paper
*golubTrain (golubTrain.rda...Training Set from the Golub Paper
Thank you.
--
Gary Lipton
http://www.linkedin.com/in/garylipton
[[alternative H…
updated 16.4 years ago • Gary Lipton
I have two RNA-seq experiments performed in different batches several months apart. Both experiments include technical replicates of the...condition A (with identical sample names: A1, A2, ..., A10). Exactly same control samples were used.
Experiment 1: 10 samples from condition A and 10 samples from condition B.
Experiment 2: 10 samples from condition A and 10 samples...from condition C.
…
of samples in normal and disease condition. I have tested that the data also contain significant batch effects with hybridization time. However, the positive hits I obtained using the following approaches are very different...NHLBI
Here eset is the expression dataset after RMA function.
__Approach 1__:
<pre>
# Consider batch effects in the model matrix
design<-model.matrix(~0+co…
updated 8.1 years ago • Xie, Zhi NIH/NHLBI [E]
I have RNA seq data an experiment consisting of an untreated and treated samples in triplicates; a total of 6 samples. The culturing of the used...shrinkage.
Q2: My data shows a strong hill shaped histogram. I am already correcting for the batch effect as this was expected to take place. Making the count-cutoff more stringent doesn’t correct fully for this effect...cts,
…
div class="preformatted">Hi,
I am using edgeR to detect differential expression in NGS experiments.
I have a brief question on what I should considered as "total size of
my
libraries".
In my case I have a set of samples...that have a quite large variation
in
the library size:
Total reads Mapped reads
1 11076283 8736308
2 5881045 4006468
3 7139703 5108608
4 9089153 5643701
5 9723103 84579…
Hello,
(I gave a lengthy explanation of my experiment here, skip to __TLDR __if so inclined)
I am working on a RNASeq experiement. I have a treatment condition which...two replicate were done at a later date. I am using deseq2 for my analysis. I have included the batch effect as a factor in my deseq2 design. After accounting for the batch, my contrast comparisons are generating nice si…
using microarray data of the
same chip type from previously published work if the
only aim of your experiment is to look at the
artifacts in your chips using the affyPLM package.
Swati
Swati Ranade
Center for Genomic Research...gt;
>
> > Hi Kawai,
> >
> > I think you might be able to generate a dummy
> training
> > set from P…
updated 20.5 years ago • Swati Ranade
Hey,
I'm running an experiment with two conditions, one is the wildtype and the other is a knock out of a gene. Each sample is from a single mouse...the samples were isolated on different days. Here is an overview
<table border="1" cellpadding="1" cellspacing="1" style="width:500px">
<tbody>
<tr>
<td>Sample</td>
<td>GT</td>
<td>Sex</td>
<…
updated 8.3 years ago • mat.lesche
<div class="preformatted">Hello everyone
I was wondering if anyone has used a tool to adjust for batch effects.
I am comparing two experiments that were done the same way over two
years.
eg.
Population 1 Treatment Control Year 1
Population 1 Treatment Control Year 2.
The same experiment, just repeated in different years.
I normalise all the cel files together (from both years) usin…
of Science, Israel
Erik Sonnhammer, Stockholm University, Sweden
and about 200 other PC-members
* *
*Paper and Poster Submission Details:
*Authors are invited to submit original research contributions or
experience reports...in English.
Paper registration and electronic submission will start in August
2006.
Submitted papers will be carefully evaluated based...on originality,
significance, te…
<div class="preformatted">Hello, everyone.
Our project is a beta tester of Affy HGU133 plus 2 chips, which
contain
56,000 probes, and the .cel file size in text format is about 32 MB.
We
currently have more than 100 chips for data process. I tried to read
in the
.cel files into my machine (1Gb RAM) and it can only read in 19 chips.
I
have been communicating with several R experts in our m…
updated 21.5 years ago • Li, Aiguo NIH/NCI
I compare an RNA-seq matrix of raw counts that I downloaded from a repository to my own RNA-seq experiment. Specifically, I want to see which samples from the downloaded paper are the closest to my samples. I have tried to...colData <- data.frame(condition = c(rep(c("A","B"), each = 2), rep(c("C","D","E"),each = 3)), batch = c(rep("1",7),rep("2",6)))`
condition batch
1 …
Affymetrix
arrays, and I
have "The Error" during the ReadAffy():
Error: cannot allocate vector of size 1770343 Kb
I know about R and OSs adressing limitations, so (according to several
posts on
the mailing list) I'm doing that...is
2^31 - 1
~ 2*10^9"
But: 2.147.483.648 = 2^31 is bigger than 1.770.343.000 bytes (my
vector size)
I'm near (above) R physical limitations?
I use batch<-…
I created an ArrayQualityMetrics report of a Large ExpressionSet. The problem is that when I move the mouse over the points of the PCA plot , the corresponding array’s metadata are not displayed in the table to the right of the plot, as they are supposed to be. Also, the data points are not responsive as they should be, when they are...mouse over the points of the PCA plot , the corresponding arr…
updated 4.0 years ago • michael.s
a separate nature and would like to combine all 41 samples in a larger analysis. The design of the experiment is basically this:
Older data - 4 separate conditions (control, negative, intermediate, positive), 5 batches
Newer...data - 1 completely different condition (diffuse), 1 batch
We know there are batch effects in the older data and would like to correct for those batch effects …
updated 9.1 years ago • schrist1
Hi all,
I am a bioinformatics novice and trying to get a handle on both conceptual and technical issues with batch effects in RNAseq datasets and analysis. The context is this:
I've done differential expression analyses in an experiment comparing responses to a drug treatment (trt, ctrl) in two populations (A, B) using both edgeR and DESeq2. Sequences for all four treatment\*population group co…
updated 7.1 years ago • rproendo
using default configuration) or if it's better to adjust it somehow. According to DESeq2 and DESeq papers, the size factors calculation with the median of ratios solves the problem of having "a few highly and differentially...happens when the overall distribution of expression for the two groups is so different. Should the size factors be adjusted by other methods?
Thank you very much in advance…
updated 7.2 years ago • Victor Barrera
condition,
levels = c("WT", "C3", "C6","C10"))
I include the batch information in my design:
pData_1$condition <- relevel(pData_1$condition, ref = "WT") # set WT as control by manual.
# input data...colData = pData_1,
design = ~ batch+condition)
The design matrix looks as follows:
> # sh…
updated 3.2 years ago • annamariabugaj
class="preformatted">Dear list,
Is there a way to optimize class weights together with the rest of
hyperparameters for SVMs in tune function (e1071)? That is, I don't
know
if tune function besides the optimization of the hyperparameters
updated 13.7 years ago • Javier Pérez Florido
colData = colData,
design = ~ Type+ batch)
dds<- DESeq(dds)
I understand that even though I included "batch" in the formula, but I still see a batch effect.
I read this...Why after VST are there still batches in the PCA plot?
The transformations implemented in DESeq2, vst and rlog , compute a variance stabilizing transformation...to remove variati…
updated 5.1 years ago • Bine
Hi all :
- When I use limma to identify differentrial expression genes , I want to correct batch effect also.
- My command and data information is :
```
> table(cluster)
cluster
control treat
368 957
> table(Exp)
Exp
p3 p4 LC05...LC09 LC10 LC11 LC12
370 587 21 210 19 69 49
> table(cluster,Exp)
Exp
cluster p3 p4 LC05…
updated 6.7 years ago • xingxd16
850K) datasets and two EPIC v.2(900K) datasets.
EPIC v.1 and v.2 datasets have different IDAT file sizes and types so, I analyzed separately using SeSaMe package.
After preprocessing, when overlapping probes are plotted...in a PCA plot, there was a significant difference between EPIC v.1 and v.2 datasets.
So when batch effect correction(using ComBat package) was performed, some beta values …
updated 19 months ago • Seungmin
Dear All,
To visualize my gene set enrichment analysis, I have been using $table$logFC from an object of class "DGELRT" as statistics argument together with two indices (index, index2). Now, I am interested...in to visualize one index using two $table$logFC lists, to display a graph with the same plot configuration as presented by Ng et al., ([Plos Genet. 2015](http://journals.plos.org...plosgen…
updated 7.9 years ago • srmaruyama
EdgeR to perform a DE analysis on 3 different treatments with 3 replicates each but I have a strong batch effect on the day of experiments.
I've been reading the manual and the example exercises (although none is exactly like...read.delim("Trinity\_trans.counts.matrix")
group<-factor(c("A","A","A","B","B","B","C","C","C"))
batch<-factor(c(4,2,3,1,2,3,1,2,3))
y<-DG…
updated 8.0 years ago • abrantes.patricia
div class="preformatted">Hello Bioconductor list server,
I am working on a microarray experiment comparing a control to a
treatment and the effects on cells. I have the results from my current
experiment and from...results_v4c4[,5]<0.05,]
I would like to find if the there are similar results from the past
experiment to the new experiment. I would like to say in the paper:
treatment A …
updated 13.8 years ago • blockaa@huskers.unl.edu
Dear Rory,
Thanks for your effort in this excellent tool! Your tutorial and detailed answers to each post are extremely helpful.
However, I feel confused to some results while running DiffBind. To better illustrate my problems, I would like to invite you to go through my case.
library("DiffBind")
samples=read.csv("res.info.csv")
tamoxifen <- dba(sampleSheet=samples)
t…
updated 3.1 years ago • littlefishes20
Hello,
I am working with RNAseq data which was acquired from experiments as following:
- PBMCs were extracted from blood of healthy donors, then extracting monocytes, pooling monocytes...were collected RNA at 4h and 24h post-infection.
- Because the heavy workload, I divided into 2 batches, each batch included 2 samples of no-infection group, 2 samples of H37Rv as control.
- Macrophages fro…
updated 18 months ago • Đình Vinh
same doses of a drug).
I guess, if the tumours are considered as replicates one could include
the batch as a factor (as you suggest below), but if they contain
different tumour classes one could not separate the dmso effect...subjects and will show strong differences per se. Maybe one get some
estimates for the impact of the batch by using a mixed effects model
with each sample as random effect …
database that has more mitochondrial DNA sequences inside of it to replace the current Silva_r138 training set.
However, the authors made this silva_metaxa2_reference_taxonomy as a qiime2 artifact (qza). The paper can be
Hi
We have two experiments run on illumina arrays done by the same company. I want to combine the data. I normally use Limmas functions (read.ilmn...and neqc) to deal with normalisation of the data. However if I combine these two experiments what is the best way of going about doing this. I am aware they need background correcting and quantile normalisation...it - i cant go into that. the compan…
updated 9.6 years ago • chris86
<div class="preformatted">Hello,
I just made my first experiences with affylmGUI and am very excited
about it. Many thanks for this!
Some questions/comments rather important to...<div class="preformatted">Hello,
I just made my first experiences with affylmGUI and am very excited
about it. Many thanks for this!
Some questions/comments rather important to me:
* With three different…
updated 20.8 years ago • SteffenMöller
user guides and various online posts, one point is still unclear (for me).
Normalization factors, size factors and how they are calculated/accessed/implemented in tximport and Deseq2.
So usually I import my samples with...tx2gene = TIDtoGID)
> dds <- DESeqDataSetFromTximport(txi,colData = sampleSheet, design = ~ Batch+AgeGroup)
> dds=DESeq(dds)
estimating size facto…
updated 4.8 years ago • svenbioinf
Dear Bioconductor Community,
based on the very interesting question on a previous post (__https://support.bioconductor.org/p/72815/__) regarding the possible batch correction methodologies, through the answers created i desided to adress a very important issue in my opinion-as im...question on a previous post (__https://support.bioconductor.org/p/72815/__) regarding the possible batch correction…
updated 10.2 years ago • svlachavas
2. Find DE genes and fold change difference between 2 Events X and Y as listed in column 3 in table below. In this case the unequal group sizes has raised some concerns by the reviewer of the study.
```
| Samples | Condition | Event...Y | 4 |
```
To my understanding DESeq2 is able to calculate DE for uneven group sizes as it calculates the group means before fold change…
updated 5.8 years ago • Zohaib Anwar
pre-processing/normalization, i created further some EDA plots, to access/investigate any putative batch effects, as i have the following information, that both healthy controls, as the disease samples belong to 3 different...phenotypes___)
So, from an initial investigation of the above 2 plots, it does not seem any severe batch effect regarding the origin/study (Additional HCs=control samples, …
updated 8.6 years ago • svlachavas
as well as different ways to compare gene expression, so it is easier for me to work with a table of transformed counts.
However, some things I've read say this is not recommended, but I haven't seen a clear explanation...does the differential expression (sorry, I didn't fully understand the differences when I read the paper, especially when blind = FALSE), then is there a way to get the coun…
div class="preformatted">Hi folks,
We are running another introductory R/Bioconductor training course
here in Seattle, Oct 9-11.
The URL is https://cobra.fhcrc.org/biocintro/
We will cover a few newer topics as well
Hi!
I'm trying to account for batch effects when comparing gene expression of my samples. My example meta data is below. All samples except for sample21...PCA.
```
(rowname) Group Tissue ConditionA PhenotypeA Combined-Condition-Tissue Batch
sample1 A brain Condition1 Phenotype1 Condition1-brain A
sample2 C liver Condition1 P…
updated 3.7 years ago • nute11a
div class="preformatted">I am looking for references to published papers on microarrays which
mention duplicate spots, i.e., replicate spots on the same array
containing
the same probe. The...that log-ratios from duplicate spots were averaged
before
further analysis. I am particularly after papers in mainline
biological
journals. Any references would be much appreciated.
Thanks a lot
Gordon&l…
Hi,
I am working with microRNA microarray data and I am facing very strong batch effetcs. In particular, I have 15 samples with a disease and 15 healthy controls. The first thing that I did was to explore...noted the presence of multiple confounding factors. Later, i looked into detail at the sources of batch effects with a PVCA, which reported that the main source of variability is due to the d…
updated 3.2 years ago • Jacopo
div class="preformatted"> BODY { font-family:Arial, Helvetica, sans-serif;font-size:12px; }Hi
All,
In the paper Exploration, normallization, and genotype calls of
high-density oligonucleotide SNP array data...an array with no MMs can accommodate features
for twice as many SNPs."
I happened to read another paper on BMC Bioinformatics, Feb 2009,
Genotype and inflated type I error rate in geno…
factors, four conditions (+/+, -/+, +/-, -/-) and four biological replicate per condition. The batch effect in this experiment comes from the fact that the first replicate for all conditions was taken separately, the...i.e. which are differentially expressed due to factor 1 alone or factor 2 alone.
(2) getting batch-free TMM-normalized FPKM values (where the batch effect has been removed). This …
updated 11.0 years ago • Ekarl2
variability analysis between two conditions (diets 1 and 2), controlling for categorical batches (e.g., sequencing days) and surrogate variables explaining non-condition/batch structure in the data. The goal is to...vst.data = vst(data, blind=F)
contrasts(seqday) <- contr.sum(levels(seqday))
batches <- model.matrix(~seqday+sv)
vst.counts.bc <- l…
Greetings all,
I've been researching ways to remove batch effects from RNA-Seq count matrices. Basically, I'm starting with a counts matrix that includes batch effects, and want...to generate a new matrix of counts that has the batch effects removed.
I'm looking to apply this to sets of RNA-Seq samples (~100 samples) that were sequenced in batches on different...all these samples in an unsuperv…
1 WT mouse, 1 "normal TG" (TGN) and 1 "disease TG" (TGD) has been sampled. This is summarized below:
---
<table border="0" cellspacing="0">
<tbody>
<tr>
<td> </td>
<td>SampleName</td>
<td>Geno</td>
<td>State</td>
<td>Mate</td>
<td>Run</td>
<td>Batch</td>
<td>Sum</td...Mate" is…
0 ~ + batch + group)`. I just wanted to know if my approach of making contrasts is correct.
My meta_data. I combined two factors (`genotype...and `treat`) into one factor, `group`.
```r
sample_name batch treat genotype group
sample1 sample1 B1 untrt WT WT_untrt
sample2 sample2 B1 trt WT WT_trt
sample3 sample3 B1 untrt...Q1.
I'd like to know tr…
Hi,
I'm currently doing a study using Affymetrix GeneChip Human Gene 1.0
ST v1.
I have a batch of 8 arrays from the first batch and 20 arrays from the
second batch. When i look at the density plot of the log2 of the
intensity...before further analysis.
I can't seem to find any information on how to procede in my analysis.
Any
experience or insight would be greatly appreciated.
Dennis
…
updated 15.6 years ago • Dennis Ting
Hello,
I'd like to run edgeR on a MeDIP-Seq experiment with 4 treatment groups (each with 5 samples). I'm counting reads in slides over the genome (a few hundred bases with...Hello,
I'd like to run edgeR on a MeDIP-Seq experiment with 4 treatment groups (each with 5 samples). I'm counting reads in slides over the genome (a few hundred bases with some overlap).
I realised that there is a small …
updated 10.1 years ago • Arne Muller
I ran some mm9 data through the HISAT2/StringTie/Ballgown RNA-seq pipeline recently and went through the listed protocol [HISAT2/StringTie/Ballgown Protocol][1]. When I used Ballgown, I was not able to identify any novel transcript isoforms as compared with Table 3 from data analyzed in the linked paper. The first thing I tried was to use no filter, but that did not work. I am wondering if there …
The [RHCSA Training Certification][1] is your ticket to becoming a Linux expert. In today's technology-driven world, mastering Linux administration...enter image description here][2]
[1]: https://www.webasha.com/courses/rhcsa-online-training-institute-certification-exam-center
[2]: /media/images/553580f8-26d8-452e-8136-4fd35970
<div class="preformatted">Dear all,
Paper describing the mathematical details about tweeDEseq package has
been published at BMC Bioinformatics
http://www.biomedcentral.com/1471-2105/14/254/abstract
The paper also compares the performance of tweeDEseq against edgeR and
DESeq under a large number of scenarios. The results obtained...div class="preformatted">Dear all,
Paper describing t…
Dear all,
I'm struggeling to find the correct approach to handling batch effects. I have a longitudinal RNA-Seq experiment where patient samples were measured in 3 batches: First the samples...from the inital visit (visit 0, batch "baseline") were sequenced, some had to be re-sequenced due to QC issues (batch "baseline_reseq") and finally the follow-up...samples from visits 1, 2, 3 came in and w…
updated 4.8 years ago • Julia
Recent ...
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