Bioconductor Forum

in which I can find the theory (included formulas and proof) beyond this approach. I read a lots of papers about this argument but in some cases they don't help me to clarify my doubts. I thank you in advance

edger

updated 8.5 years ago • erika_lilly

www.ebi.ac.uk/goldman-srv/rlsim/. But the latest version of rlsim is 2014. And the corresponding paper seems to be a BioRxiv article from 2015... which seemingly has never been published. Thank you in advance. RM

rna-seq reads

updated 6.5 years ago • Ramiro Magno

trying to estimate the variability technical replicates from different microarray platforms. The few papers I found on this topic and current opinion seems to suggest that technical replicates are not required for microarrays

Microarray Microarray

updated 17.7 years ago • Adaikalavan Ramasamy

It looks like DESeq2 has been used efficaciously for MS data in published papers (<https://www.ncbi.nlm.nih.gov/pubmed/?term=26193490>).  However, that is for unlabeled MS data, in which the only information

deseq2

updated 8.5 years ago • maduanduan8

method is used for specific data type, such as steady-state or time course. Is there a evaluation paper on this topic? Best, Pengcheng

minet build.mim

updated 8.9 years ago • Pengcheng Yang

it into a flowFrame, so far I've just being able to do this (by following the instructions from a paper from BD): set.sub <- fsApply(fs, function(x) {samp <- sample(1:10000, size = 100) set.sub<-new('flowFrame',exprs = x\[samp,\])}, use.exprs

bioconductor flowcore sample

updated 9.4 years ago • cherryzt

The paper "Oldham, M.C., P. Langfelder and S. Horvath, Network methods for describing sample relationships in genomic datasets: application

wgcna wgcna package

updated 7.3 years ago • 2323982403

Learning and Applications (ICMLA 2009)" to be held in Miami, Florida, USA, 13-15 Dec. 2009. The paper submission seadline is: July 15, 2009. More details at: http://www.icmla-conference.org/icmla09/CFP_SpecialSession8.html

updated 16.5 years ago • Tarca, Adi

<span style="line-height:1.6">Hi,</span> Somatic signatures package uses RSS and unexplained variance to assess the best number of signatures. In Alexandrov et al paper (Cell Reports 3, 246-259) they used cosine similarity and Frobenius reconstruction error to determine the number of signatures...uses RSS and unexplained variance to assess the best number of signatures. In Alexandrov…

somaticsignatures

updated 10.3 years ago • Asma rabe

https://rnbeads.org/data/install.R') Bioconductor version 3.14 (BiocManager 1.30.16), R 4.1.0 (2021-05-18) Installing package(s) 'RnBeads' also installing the dependencies ‘gsl’, ‘genefilter’, ‘GSEABase’, ‘lumi’, ‘aws’, ‘IlluminaHumanMethylationEPICanno.ilm10b4.hg19

Epigenetics RnBeads R

updated 3.8 years ago • nabiyogesh

c("RRM2", "BIRC5", "TOP2A")) : DGIdb service not available. sessionInfo( ) R version 4.1.2 (2021-11-01) Platform: x86_64-pc-linux-gnu (64-bit) Running under: Ubuntu 20.04.3 LTS Matrix products: default BLAS: /usr/lib/x86_64

rDGIdb

updated 3.9 years ago • DannyM

a1) : could not find function "colMax" ?colMax sessionInfo() R Under development (unstable) (2021-01-28 r79891) Platform: x86_64-apple-darwin17.0 (64-bit) Running under: macOS Mojave 10.14.6 Matrix products: default BLAS

xcms

updated 4.6 years ago • Habil Zare

Hello, I'm reading the DESeq2 paper, and i have two questions regarding the prior for LFC. 1) For the variance of the normal prior for LFC, I am wondering why...Hello, I'm reading the DESeq2 paper, and i have two questions regarding the prior for LFC. 1) For the variance of the normal prior for LFC, I am wondering why the

DESeq2

updated 6 months ago • Chenghao

counts in CPM. **But what is the actual normalization method used?** I am going along using this [paper][1]... so is it normalisation by distribution it uses or by library size? Any help to understand this is highly appreciated

DEGUST Normalization CPM

updated 4.2 years ago • Caroline

the results of my pipeline with previously published experiments but I dont seem to find any papers using the current version of DESeq2 (v1.30.0) with available reads. I found that installing previous versions of DESeq2

DESeq2

updated 4.9 years ago • Samuel Daniel

<div class="preformatted"> Friends, Could you, please, help me to find gene expression meta analysis tutorial. I have several microarray studies and need to combine them. I am not bioinformatician/biologist, so I need really step-by-step instructions. Sometimes, authors supply their papers with step-by-step instructions. I need something that will work, and I don't carry about quality of r…

Microarray Microarray

updated 11.6 years ago • Guest User

Hello, I'm trying to use EBseq-HMM to analyze some time course data. In my case I have 12 time points with 3 biological replicates, 36 samples in total. When I run the pipeline, it seems that it needs an lot of resources, running it in a cluster asking for 64gb of ram does't seem to be enough to finish de analysis. The resources needed to run this pipeline are not discussed in the paper and I ju…

ebseq-hmm

updated 9.8 years ago • liamarseg

Hi Michael, I've read you paper on DESeq2 (Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2) and have a question about

deseq2

updated 9.7 years ago • ilyaal

Hi, I am using DRIMSeq / DEXSeq-DTU workflow describe by Love at al. 2018. According to the paper, 'scaledTPM' option is chosen for normalisation (latter on 'dtuScaledTPM' option was added to the tximport package). 1) What

tximport DEXSeq-DTU DRIMSeq

updated 5.5 years ago • aleksandar.baburski.g

ST 1.0 array, I have been tried to search existed packages for process this kind of data. There is a paper "Comprehensive Analysis of Affymetrix Exon Arrays Using BioConductor" descried the package 'exonmap' seems no longer

PROcess PROcess

updated 11.7 years ago • Guest User

Hi, I have followed [this](https://f1000research.com/articles/5-1438/v2) paper but I have problem to undestand the following piece of code: > pch <- c(0,1,2,15,16,17) > colors <- rep(c("darkgreen", "red", "blue

edger plotmds

updated 8.2 years ago • mictadlo

find for the microorganism I am working with i.e. *Clostridium beijerinckii* NCIMB 8052. I have read paper and information about it that it is a number to identify genes specifically but I am struggling with finding the source

annotation

updated 6.2 years ago • mnazir

div class="preformatted">some have asked me about a reference for gcrma... a paper is now officially accpeted by the journal of the american statistical association (JASA). you can get the info here: http

gcrma gcrma

updated 21.4 years ago • Rafael A. Irizarry

itself. e.g. SP1 gene is interactiong with itself or have a loop or activating. i need reference paper or tool or website link just to use for reference. Please guide me ASAP. if anybody is interested but dn't want to give &nbsp

microarray gene interaction geneexpression

updated 9.0 years ago • shaheryar

how did you calculate the "baseMean counts" in the output of DESeq2. I looked the Genome Biology paper and additional files, it seems you used mean counts or mean expression there. If you give the "baseMean counts" as an output

deseq2

updated 10.0 years ago • zpingfeng

or "KO~"WT". I tried both way, the results are quite different. The way described in the original paper on how GSEA works does not seem give an excuse how this parameter affect the results, and why this happened. Please help

updated 13.7 years ago • wenhuo hu

fold-change is greater than 1.5 (on a log2 scale). For the estimated fold change, does the paper mean that avg_logFC > 1.5 or FC > 1.5 and avg_logFC > 0.58 (knowing that log2(1.5) = 0.58)? Also, it is not clear to me how the

MAST

updated 6.0 years ago • ahmed.abbas

div class="preformatted">Hi, All: As part of the suggestions from a reviewer of my submitted paper, I am asked to provide the IM (Ideal Mismatch) values generated from MAS5 for some probes of some probeset. I know BioConductor

updated 18.8 years ago • Wang, Yonghong NIH/NCI

oligonucleotide array probe level data. Biostatistics. 2003 Apr;4(2):249-64. and a number of other papers by the same first author. David Rocke and Blythe Durbin have a number of papers, as far as I know they, as well as Trey Ideker

Normalization Cancer probe Normalization Cancer probe

updated 22.3 years ago • Wolfgang Huber

<div class="preformatted">Dear Bioconductors, In evaluating several RNA-seq analysis techniques, I decided to analyse the same SEQC spiked-in dataset as mentioned in the limma-Voom paper (Law et al. 2014, Genome Biology). This dataset contains 92 genes, 69 of which are spiked-in at different concentrations. As in the paper, I copied the 23 non DE genes twice, providing me a dataset with a …

PROcess PROcess

updated 11.8 years ago • Koen Van den Berge

to integrate using MNN_correct and then perform DE, reproducing the method presented in the [MNN paper][1]. I would appreciate your opinion on my rationale. I have processed both datasets and then corrected using mnn_correct...variable (GSE1, GSE2) X the feeding condition variable (Fed, FD). [Reproducing the logic of the paper][2]. My aim is to get the effect of food deprivation for this cell …

Scran MNN_correct Differential expression single-cell

updated 6.7 years ago • baldissera152

Hi, I'm attempting to download the datasets that go with the paper ["Clinical utility of microarray-based gene expression profiling in the diagnosis and subclassification of leukemia...with the R package GEOQuery. There are two datasets (stage 1 and 2) associated with the research paper, and the and I've been using these commands to download them both: <pre> <strong>>librar…

software error geoquery

updated 8.4 years ago • mmayo

<div class="preformatted">Dear limma experts, I am analyzing the data set given to me and described by these the column names of my MA object: > colnames(MA.hyp) [1] "../ampcon/mev/C0-_1stround_vs_C60-_1stround_13263536.mev" [2] "../ampcon/mev/C0-_2ndround_vs_C60-_2ndround_13263534.mev" [3] "../ampcon/mev/C60-_1stround_vs_C0-_1stround_13263533.mev" [4] "../ampcon/mev/C60-_2ndround_…

limma limma

updated 19.4 years ago • Andrew Mcdonagh

of replicates and samples are less than or equal to 5. We upgraded the LPE package from the original paper (2003), and published a paper in BMC Bioinformatics. The latest version is on Bioconductor since early last year. (http://www.biomedcentral.com...question: How can one run simply the Bonferroni adjusted LPE test from your 2003 Bioinformatics paper (Figure 2 and page 1948), using the LPE R p…

LPE LPE

updated 19.8 years ago • Jain, Nitin

the form at [https://forms.gle/bSRaA2btAEsYDiCN9][2]. Applications close on Friday 26th February 2021. Questions about the role can be directed to current board members (contact details can be found at [https://bioconductor.org

bioconductoroversight community BiocVersion news

updated 4.8 years ago • Matthew Ritchie

indicating differences in the distributions? On the one hand, the smooth quantile normalization paper seems to imply this. On the other hand in previous posts Gordon Smyth has stated that TMM is usually the best way to proceed

limma-voom smooth-quantile-normalization quantro

updated 3.4 years ago • raf4

examples of people filtering out immunoglobulin genes during RNA-seq analysis, such as in this paper : https://www.nature.com/articles/s41467-019-11373-9 However, I am interested in the immunology of the condition I am studying

RNASeq

updated 4.3 years ago • maria.papanikolaou

I'd like to get a precise and intuitive understanding of how empirical Bayes moderation (conducted by `eBayes` function of the `limma` package) in the `limma` analysis pipeline works. I tried to read through the [original paper](https://www.degruyter.com/document/doi/10.2202/1544-6115.1027/html) but found it too technical and time-consuming. Could...the `limma` package) in the `limma` analysis pi…

limma

updated 4.5 years ago • Junghoon

have been prepared with the small sample target protocol for the human plus2.0 chip I remember of a paper by Irizzary on a modified RMA for small samples. Can someone give a suggestion on the analyse to run, better the classical

updated 18.0 years ago • marco fabbri

div class="preformatted">Hi I was just browsing through my collection of papers and came across this one: http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&d op t=Abstract

Microarray limma Microarray limma

updated 21.3 years ago • michael watson IAH-C

Dear all, I have found this paper: [piRNAs Are Associated with Diverse Transgenerational Effects on Gene and Transposon Expression in a Hybrid Dysgenic

deseq2

updated 9.5 years ago • ribioinfo

outliers in these part of the spectrum but what else if they are excluded from analysis ? Is there a paper / study which deals with the distribution of gene expression for extreme values that somebody can suggest me ? thanks

updated 21.2 years ago • Phguardiol@aol.com

to use loess normalization function based on externals controls (like MSP) as in Yang et al.; 2002 paper. I work with bioconductor marrayNorm package. I identified my controls in the maControls structure of marrayLayout

Normalization Normalization

updated 21.6 years ago • Ghislaine Guigon

Hi Julie, I have read a paper titled "Genome-scale measurement of off-target activity using Cas9 toxicity in high-throughput screens",and have found

annotation

updated 6.1 years ago • XIN1988

values of log2folchange were lower than 1 (the MA plot is attached). Now I started to write my paper and I saw that several authors used log2foldchange > 1 as cutoff to downstream analysis as functional analysis. Do

deseq

updated 11.1 years ago • acesar

for security reasons. Does anyone have a copy of Bioconductor on CD-ROM they can send me by paper mail (p-mail), and then could I load the code from the CD-ROM into R? (Presumably I'd need to script to load into R?) Thank you for

updated 20.1 years ago • jro203

can get a pretty good idea of how to proceed by working through the supplementary material of the paper, it has it's own repos at: Also Sophie there is a github thread for phyloseq with deseq at: http://joey711.github.io/waste

DESeq phyloseq DESeq phyloseq

updated 11.7 years ago • Susan Holmes

<div class="preformatted">Hello all, I know this has probably been asked several times, but would anybody know of a little textual description of how RMA works? I am very familiar with the papers on the issue, but would anybody know of a simplified text that one could use to explain the method to people that are not...but would anybody know of a little textual description of how RMA works? …

updated 21.2 years ago • Lawrence Paul Petalidis

in edger one gets lots of values <1. Unfortunately, I found neither in edger manual nor in edger paper the description how the log fold change is calculated. Especially how those values <1 are treated because for instance

edger normalization logfc

updated 9.9 years ago • tonja.r

div class="preformatted">hi, A few papers have concluded that DESeq is more accurate for DE genes discovery than methods using FPKM, and that the bias in FPKM

Visualization DESeq Visualization DESeq

updated 12.4 years ago • Jike Cui

div class="preformatted">Dear All, Recently I found an interesting paper about problems with RMA when applied to small sample sets which are based on the median-polish algorithm, see: http://www.biomedcentral.com

updated 15.0 years ago • cstrato

An embedded and charset-unspecified text was scrubbed... Name: not available Url: https://stat.ethz.ch/pipermail/bioconductor/attachments/20071019/ 9166f717/attachment.pl

updated 18.2 years ago • Ana Conesa

<div class="preformatted">In the paper: Exploration, Normalization and Summaries of High Density Oligonucleotide Array Probe Level Data the following statement...div class="preformatted">In the paper: Exploration, Normalization and Summaries of High Density Oligonucleotide Array Probe Level Data the following...be "before gcrma". This explanation made sense to me, but seems to contradic…

Normalization probe Normalization probe

updated 19.5 years ago • noel0925@sbcglobal.net

height:355px; width:1038px"/> I did look at the vignette, the documentation, the sashimi plot paper https://academic.oup.com/bioinformatics/article-abstract/31/14/2400/254271/Quantitative-visualization-of-alternative...s when I realized the meaning of the Y-axis label (which is not part of the original sashimi plot paper). So, I just want to make sure that we got the interpretation correctly…

Gviz

updated 9.0 years ago • Leonardo Collado Torres

<div class="preformatted">Dear limma experts I am analyzing the data set given to me and described by these the column names of my MA object: > colnames(MA.hyp) [1] "../ampcon/mev/C0-_1stround_vs_C60-_1stround_13263536.mev" [2] "../ampcon/mev/C0-_2ndround_vs_C60-_2ndround_13263534.mev" [3] "../ampcon/mev/C60-_1stround_vs_C0-_1stround_13263533.mev" [4] "../ampcon/mev/C60-_2ndround_…

limma limma

updated 19.4 years ago • Andrew Mcdonagh

div class="preformatted">Hi, is there any paper or explanation of how should I interpret heatmap with dendrogram. symbs <- getSYMBOL(myFeatureGenes,"moe430a"); symbs

updated 21.2 years ago • SAURIN

significance of a result assuming some prior rate of false discovery (type 1 error). I read the 1995 paper for the BH method but I am still confused on what exactly determines this rate? Is it done in a parametric way or non-paramterically

Microarray Microarray

updated 12.4 years ago • Cornish, Joseph NIH/NIAID [F]

isoform level information (situation similar to that shown in Figure 1C of the Sonenson et al paper on the tximport package). I am trying to find the best set of parameters for DE analysis. Is it better to use the transcript

tximport DESeq2 "tximport" deseq2 salmon

updated 8.5 years ago • sunil.mangalam

from the community. I have searched the internet but found just a couple of discussions and papers about selecting control genes (i.e. housekeeping) for real time pcr verification of microarrays results, but nothing

Microarray Microarray

updated 19.6 years ago • Mike Ferker

from origins. From reading the vignette this application seems fine, but after reading the original paper we weren't so sure. Thank you, Adam Cornwell [[alternative HTML version deleted]] </div

RankProd RankProd

updated 12.9 years ago • Cornwell, Adam