Bioconductor Forum

as the test statistic for gene set enrichment analyses when running the fgsea package. I have seen a paper that suggests the absolute value of Signal-To-Noise is a better metric than LFC: https://bmcbioinformatics.biomedcentral.com

apeglm fgsea Signal-To-Noise Ratio

updated 6.6 years ago • coulsonr

entrez/query.fcgi?cmd=Retrieve&db=pu bmed&dopt=Abstract&list_uids=12112249">this paper</a> useful. --Dennis Hi I have one other question is there an article somewhere which explains in a manner a non statistician

limma limma

updated 21.6 years ago • Dennis Hazelett

reperfrom a poisson distribution test that was presented in a recent-published biological research paper (Plant Physiology 2008, vol 148, pp. 1189-1200). That test is about the occurrence number of a kind of gene in separate chromosomes

updated 16.4 years ago • Mao Jianfeng

tools. But I wonder what's the recommended way to run cufflinks tools. I've read the spliceR paper and bioConductor vignette, but could not find the related information. specifically: 1. is novel annotation necessary

Annotation spliceR Annotation spliceR

updated 10.5 years ago • hliang

<div class="preformatted">Hi, I am currently processing Infinium HumanMethylation450K BeadChips. While looking for all the necessary steps I read the paper 'A comprehensive overview of Infinium HumanMeththylation450 data processing' by Dedeurwaerder et al. There they say...Infinium HumanMethylation450K BeadChips. While looking for all the necessary steps I read the paper 'A comprehensive o…

updated 12.1 years ago • Aileen Chefai

Hi everyone, I am comparing different proteomes from fractionation experiments. No SILAC was used, only LFQ. I started to analyze the data with the DEP package, only to find out that the adjusted p.value were very high for almost all proteins. The original paper, where the package was developed, says "*the fraction of differentially enriched proteins should not exceed 10–15% of the...only to…

dep proteomics limma

updated 5.9 years ago • Rob

The [InTAD paper][1] states `InTAD can be applied to any heterogeneous cohort of samples analyzed by a combination of gene expression...The [InTAD paper][1] states `InTAD can be applied to any heterogeneous cohort of samples analyzed by a combination of gene expression and

InTAD

updated 6.4 years ago • ATpoint

http://www.bioconductor.org/packages/2.11/bioc/html/bsseq.html And the associated Genome Biology paper: http://genomebiology.com/content/pdf/gb-2012-13-10-r83.pdf From what I can see the method should work on reduced representation

Sequencing bsseq Sequencing bsseq

updated 12.8 years ago • Alex Gutteridge

Website: www.xcelrisgenomics.com "Please don't print this e-mail unless you really need to. Save Paper, Save Trees" ---------------------------------------------------------------------- ---------- Disclaimer\ \ \ Any views or opinions presented in this...{{dropped:13}} </div

crlmm crlmm

updated 14.0 years ago • Chintan Vora - Xcelris

https://bioinformatics.oxfordjournals.org/content/early/2014/01/28/bioinformatics.btu049.full.pdf) paper (Fig. 5-6A) and also the origianl bump hunting [manuscript](http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3304533/pdf/dyr238.pdf

minfi bumphunter 450k region

updated 9.0 years ago • cardenasca

on the plot. I noticed that they are also present on the example MA plots in the Cope, et.al (2005) paper. I have been unable to find an explanation of what these mean, and would appreciate it if someone could tell me what they

affycomp affycomp

updated 19.7 years ago • McGee, Monnie

of transcripts: 35367 # Db created by: GenomicFeatures package from Bioconductor # Creation time: 2021-03-18 12:37:55 -0600 (Thu, 18 Mar 2021) # GenomicFeatures version at creation time: 1.42.2 # RSQLite version at creation time: 2.2.4...of items to replace is not a multiple of replacement length** > sessionInfo() R version 4.0.4 (2021-02-15) Platform: x86_64-apple-darwin17.0 (64-…

Aspli ASpli

updated 4.6 years ago • jbono

power.t.test will probably not get you directly to your desired result. There have been numerous papers that attempt to define exactly what you are trying to define (at least if I understand you correctly). You might start...that to reflect a ref design? Is what I'm trying to achieve feasible at all? Because I read another paper saying that the effectiveness of the loop design becomes less if y…

updated 19.1 years ago • Sean Davis

<div class="preformatted">i'd like to repeat what was done as part of: 'Summaries of Affymetrix GeneChip probe level data' by Irizarry et al. Nucleic Acid Res., 2003, 31(4):e15 http://nar.oupjournals.org/cgi/content/full/31/4/e15 that is, compare the Affymetrix I/D/NC calls/p-values for a differential expression experiment involving just 2 arrays with those based on the RMA method. in the…

Normalization probe affy affyPLM Normalization probe affy affyPLM

updated 20.8 years ago • Reiner Schulz

I am trying to analyse a two colour micro array data. I was trying to reproduce the results in the paper (http://www.ebi.ac.uk/arrayexpress/experiments/E-MTAB-120/ ). In this paper, the authors say that they have normalized the

Normalization limma siggenes

updated 11.3 years ago • Guest User

1 orthologous exons, and I'm aiming at detecting DE exons between species. After reading the "voom" paper (http://www.statsci.org/smyth/pubs/VoomPreprint.pdf), I am leaning towards using this approach rather than count-based...length, so I was looking for some way to correct for exon length when testing for DE. In the voom paper it is mentioned that although voom is based on log-cpm values, it "/…

Genetics DESeq Genetics DESeq

updated 12.5 years ago • Julien Roux

<div class="preformatted">i'd like to repeat what was done as part of: 'Summaries of Affymetrix GeneChip probe level data' by Irizarry et al. Nucleic Acid Res., 2003, 31(4):e15 http://nar.oupjournals.org/cgi/content/full/31/4/e15 that is, compare the Affymetrix I/D/NC calls/p-values for a differential expression experiment involving just 2 arrays with those based on the RMA method. in the…

Normalization probe affy affyPLM Normalization probe affy affyPLM

updated 20.8 years ago • Reiner Schulz

using the code below but cannot retrieve it. I found this modified manifest useful from recent paper; https://bioconductor.org/packages/devel/data/annotation/vignettes/EPICv2manifest/inst/doc/EPICv2manifest.html

DNAMethylation AnnotationHub EPICv2manifest annotation

updated 20 months ago • s.malik

Dear all, I'm trying to find the package CompStatViz which has the scripts used in the paper of bepress "Visualizing Genomic Data (February 1, 2006) Robert Gentleman, Florian Hahne, and Wolfgang Huber". In the bepress

updated 19.6 years ago • Diego Diez

if there is an up or down regulated gene which P value is significant and how do I report them in paper. Thanks

deseq

updated 8.6 years ago • Shrikant Pawar

I was reading this paper from 2010 : [https://bmcbioinformatics.biomedcentral.com/articles/10.1186/1471-2105-11-94#Sec11][1] [1]: https://bmcbioinformatics.biomedcentral.com

DESeq2 sequencing

updated 4.7 years ago • simplyphage

than 10M per sample, in comparison with some samples I got before, which had 30-35M per sample). The paper is here: https://www.nature.com/articles/nmeth.f.376.pdf I know that, in addition to sequencing depth, we should also

deseq2

updated 6.7 years ago • andrebolerbarros

using conditional quantile normalization. Johns Hopkins University, Dept of Biostatistics Working Papers, 227 (2011). http://www.bepress.com/jhubiostat/paper227 Kasper Daniel Hansen, Rafael Irizarry and Zhijin (Jean) Wu </div

Normalization cqn Normalization cqn

updated 14.4 years ago • Kasper Daniel Hansen

<div class="preformatted">Gaurav, You could use the following code to read in your peak file where ~/dataset/peaks1.bed contains the peaks in bed format. Library(ChIPpeakAnno) peaks1= BED2RangedData(read.table("~/dataset/peaks1.bed", sep="\t")) For detailed information on how to use ChIPpeakAnno, please type vignette("ChIPpeakAnno") Also, you might want to read the paper http://www.biom…

annotate ChIPpeakAnno annotate ChIPpeakAnno

updated 12.7 years ago • Julie Zhu

Hello everyone, i want to adjust some features within the CRISPRseek package for Cpf1. Can somebody tell me more about the Argument gRNA.backbone and the subPAM.activity ? I don't know how the arguments work and need a further description as in the paper Package "CRISPRseek" from May 26. Maybe somebody knows where i can get those further descriptions or can help me with the...the subPAM.activ…

CRRISPRseek gRNA.backbone subPAM.activity rule.set

updated 5.5 years ago • nils.hassel

on lumi package that you developed and I am going to apply it to my HM450K dataset and put your paper as citation. Can I have a simple question on reading file? As your example file is different from what I got with HM450K

Cancer lumi Cancer lumi

updated 13.7 years ago • Hu, Xin

Dear Bioconductor community, i have some gene expression microarray data, on which i would like to fit a machine learning methodology and construct a classifier regarding a binary outcome(Disease status). Although from literature and various papers i have found various packages and methodologies in R, as i would like also to add additional continuous variables alongside...a classifier regarding …

classification machinelearning microarray multivariate caret

updated 10.1 years ago • svlachavas

destiny’ is not available for Bioconductor version '3.13' sessionInfo( ) R version 4.1.0 (2021-05-18) Platform: x86_64-w64-mingw32/x64 (64-bit) Running under: Windows 10 x64 (build 18363) Matrix products: default locale

destiny

updated 4.4 years ago • chet.seligman

for the 2-level group variable (control=0, case=1). I have used the R codes that Hamel Patel (2021) Scientific Reports and published at: https://zenodo.org/record/3895886#.YJKg893RbDc I refrain from pasting the codes

lmFit

updated 4.6 years ago • AyHi

Course: Proteomics Using R/Bioconductor ONLINE, 15-17 March 2021 Instructor: Dr. Laurent Gatto (de Duve Institute, UCLouvain, Belgium) Course website: https://www.physalia-courses.org...Course: Proteomics Using R/Bioconductor ONLINE, 15-17 March 2021 Instructor: Dr. Laurent Gatto (de Duve Institute, UCLouvain, Belgium) Course website: https://www.physalia-courses.org/courses

ProteomicsWorkflow proteomics Proteome

updated 5.0 years ago • info

sneumann/mzR/wiki/mzR-Rcpp-compiler-linker-issue. ``` Output sessionInfo: ```r R version 4.0.4 (2021-02-15) Platform: x86_64-w64-mingw32/x64 (64-bit) Running under: Windows 10 x64 (build 19042) Matrix products: default locale

mzR

updated 4.7 years ago • Sarah

distinguish between up- and down-regulated genes). ![https://i.postimg.cc/s2p1b80p/Screen-Shot-2021-04-18-at-12-03-14-PM.png][1] Do I somehow need to scale the data before plotting it? Thanks for any advice. [1]: https://i.postimg.cc...s2p1b80p/Screen-Shot-2021-04-18-at-12-03-14-PM.png

Heatmap ComplexHeatmap colorRamp

updated 4.6 years ago • Assa Yeroslaviz

An embedded and charset-unspecified text was scrubbed... Name: not available Url: https://stat.ethz.ch/pipermail/bioconductor/attachments/20060209/ 6cdba420/attachment.pl

updated 19.8 years ago • Alvord, Greg DMS [Contr]

<div class="preformatted">Hi Martin, There are quite a few packages that deal with least squares analysis - also partial least squares. In the latter case there is even one package that is expressly for microarray / gene expression data: the package name is plsgenomics - you can download it from CRAN and it will take your data as is (experiments in columns, genes in rows). Also there is …

Microarray cycle Microarray cycle

updated 17.2 years ago • Amy Mikhail

is this a valid approach to this problem? Or should more time be spent on normalization. In the Csaw paper, DiffBind paper, and the Csaw book there is a lot of emphasis placed on normalization strategies. For this ChIP we are not

csaw ChIPseq DESeq2 DiffBind

updated 9 months ago • Luca

reaching out with questions regarding the filtering step prior to running the ProActiv tool. In your paper, in the "Identification of tissue-specific alternative promoters" section, you mentioned that "we filtered out inactive

Transcriptomics proActiv

updated 13 months ago • LuciaNhu

just treatment vs. control. Also, I would appreciate it if you could provide examples of scientific papers where this issue was addressed and the correct correction method was applied to a real scientific problem and data

DESeq2 MultipleComparison r

updated 3.0 years ago • ncorak

Methylation=="Un"] ``` Could You explain to me the difference between both approaches? In other papers, there are also two different approaches. Regards

RRBSdata edgeR methylationArrayAnalysis

updated 2.4 years ago • Krzysztof

The [DESeq2 paper, page 15](http://genomebiology.biomedcentral.com/track/pdf/10.1186/s13059-014-0550-8) explains the first of the three

deseq2 negative binomial model glm

updated 7.4 years ago • jeremy.teitelbaum

log.it = TRUE, verbose = TRUE, span = 2/3, family.loess = "symmetric") one of the paper said normalize.loess(data,epsilon=1,log.it=F,span=0.4,maxit=2). The data for epsilon,log.it,span and maxit have to be as

Microarray Microarray

updated 15.1 years ago • viritha kaza

Dear there, From the TCGAbiolinks paper (https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1006701), I see it need scaling Recount2...Dear there, From the TCGAbiolinks paper (https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1006701), I see it need scaling Recount2 data

TCGAbiolinks RECOUNT2 DESeq2

updated 4.7 years ago • xiaofeiwang18266

I could not find any online methods for this sort of analysis, though its been shown in many papers. Thanks

atac-seq atac deseq2 sva combat

updated 8.8 years ago • g.atla

I have a question about how to derive the gene centric values for the probe set: When reading the paper I saw this description: "From the methods (Microarray Experiments): Probes on all three platforms were aligned to a transcript

cdf cdf

updated 14.7 years ago • Xiaowei Guan

Hello list In the recent  limma paper (Nucleic Acids Research 2015) it was mentioned that limma is applicable for analyzing Nanostring data. I have nanostring

nanostring limma

updated 10.6 years ago • mali salmon

div class="preformatted">Dear Christian: I am new to XPS and following your paper on comparing XPS with APT. I used the listed code to create scheme object: Scheme.HuEx10stv2r2.na27=import.exon.scheme

xps xps

updated 15.7 years ago • Lisa Mu

package vignette and the following tutorial from CSAMA2015, but are there any additional workflow papers or other resources that might be helpful to me in setting this up? http://www.bioconductor.org/help/course-materials

ebimage

updated 9.2 years ago • phil.chapman

00036.21 Dudoit and Fridlyand (2003) Bioinformatics 19(9) 1090-1099 Clest is outlined in the first paper Regards Peter -- Dr Peter Baker, Statistician (Bioinformatics/Genetics), CSIRO Mathematical & Information Sciences

updated 22.1 years ago • Peter Baker CMIS, Indooroopilly

Hi, In the Nat Prot paper about Ballgown, it's said: _Note that Ballgown’s statistical test is a standard linear model-based comparison. For small

ballgown limma

updated 8.5 years ago • rodri2006

I recommend and do it this myself. It's such common practice that it's surprising to see a paper on it at this stage. It is in the spirit of normalization methods that all probes should be retained for normalization...Re: [BioC] Filtering before differential expression analysis > of microarrays - New paper out > To: Daniel Brewer <daniel.brewer at="" icr.ac.uk=""> &…

Microarray Normalization GO probe vsn limma Microarray Normalization GO probe vsn limma

updated 16.9 years ago • Gordon Smyth

the results of running the following in an R session 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

GSVA SingleCellData

updated 3.7 years ago • Amna

**Biostatistics research associate in the University of York, United Kingdom** Application deadline: 26/05/2021 https://jobs.york.ac.uk/wd/plsql/wd_portal.show_job?p_web_site_id=3885&p_web_page_id=442112 Applications are...research associate in the University of York, United Kingdom** Application deadline: 26/05/2021 https://jobs.york.ac.uk/wd/plsql/wd_portal.show_job?p_web_sit…

QTL fourier TimeSeriesExperiment timecoursedata

updated 4.7 years ago • Daphne

m completely lost. Can anyone be of assistance? sessionInfo( ) ``` R version 4.0.5 (2021-03-31) Platform: x86_64-apple-darwin17.0 (64-bit) Running under: macOS High Sierra 10.13.6 Matrix products: default BLAS

org.Mm.eg.db

updated 4.6 years ago • Jack

Dear all, Based on the following paper by Dr. Hicks (https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6547503/), I tried other ways to adjust for multiple testing

qvalue

updated 3.8 years ago • mikhael.manurung

most parametric models don't seem to be a good fit for my problem. I was looking into the `voom` paper and am wondering if it is statistically sound to apply linear mixed models to the `voom` transformed data using external

stats r RNASeqData limma voom

updated 2.0 years ago • pl23

getAnnotation For detailed information on how to use the package, please refer to the paper in BMC Bioinformatics (http://www.biomedcentral.com/1471-2105/11/237) and ChIPpeakAnno practical presentation given

Annotation ChIPpeakAnno Annotation ChIPpeakAnno

updated 15.2 years ago • Julie Zhu

I have been assuming that the base of the B-value log in Limma = 2, but I recently reread the paper and didn;t see a base. Is the base 2, and if not what is it/ Thanks and best wishes, Rich ------------------------------------------------------------ Richard A. Friedman, PhD Associate Research

Cancer limma Cancer limma

updated 8.4 years ago • Richard Friedman

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

deseq2 quantro normalization

updated 7.2 years ago • Victor Barrera

able to incorporate lfcThreshold into calculation of null. What bothers me is that all published papers are using simple comparisons, at least in plant science, but all, test against non-zero log fold change. If me using ashr

ashr Deseq2 lfcThreshold

updated 5.6 years ago • Iryna

<div class="preformatted">Hello, I am trying to replicate results in a published paper, where they performed a MAS5.0 normalization with the median normalized to 50 and then defined genes as present if the...div class="preformatted">Hello, I am trying to replicate results in a published paper, where they performed a MAS5.0 normalization with the median normalized to 50 and then defined…

Normalization Normalization

updated 15.0 years ago • Matthew Willmann

<div class="preformatted">1. Has anybody tried to port WebbioC to WindowsOS? 2. I have read paper and literature regarding "SAM" description but still do not understand it completely. Kindly, someome could spare a little...div class="preformatted">1. Has anybody tried to port WebbioC to WindowsOS? 2. I have read paper and literature regarding "SAM" description but still do not understa…

webbioc webbioc

updated 19.8 years ago • Narendra Kaushik