Bioconductor Forum

but not in DESeq. I actually get the opposite. Can you help with this please? Also, in the publication of the diffbind EdgeR was the default. Now DESeq2 is the default. Do you have any preference to one of the methods

diffbind normalized counts

updated 9.5 years ago • GFM

best wishes Robert -- Robert Gentleman, PhD Program in Computational Biology Division of Public Health Sciences Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N, M2-B876 PO Box 19024 Seattle, Washington

Cancer Cancer

updated 18.2 years ago • rgentleman

best wishes Robert -- Robert Gentleman, PhD Program in Computational Biology Division of Public Health Sciences Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N, M2-B876 PO Box 19024 Seattle, Washington

Cancer Cancer

updated 19.4 years ago • rgentleman

1.8.4) the ACCNUM mappings correspond to the GenBank accession numbers from the 'Representative Public Identifier' field of the Affymetrix csv format annotation files, whereas in the 3 previous releases (moe430a and rae230a

Annotation moe430a rae230a Annotation moe430a rae230a

updated 20.5 years ago • MARIA STALTERI

<div class="preformatted"> I would like your suggestion for the bioinformatics approaches how to select biomarker genes in the cancer cell lines. We have IC50 data for a compounds screening to about 100 cell line, resulted in compound sensitive or resistant for the cell lines. We would like to have tool to select gene or marker correlated with the gene expression or copy number changes. How…

Cancer Cancer

updated 12.0 years ago • Guest User

Regards Aedin -- Aed?n Culhane, Research Associate in Prof. J Quackenbush Lab Harvard School of Public Health, Dana-Farber Cancer Institute Web URL: http://www.hsph.harvard.edu/researchers/aculhane.html </div

Cancer Cancer

updated 19.0 years ago • Aedin Culhane

am able to use the RStudio AMI through http port 80, I would also like to be able to tunnel the AWS public DNS to a localhost (as I have done many times previously). However, the AMI does not seem to provide for SSH tunneling to

RStudio AWS AMI

updated 6.5 years ago • bio-explorer

it. thanks Robert -- Robert Gentleman, PhD Program in Computational Biology Division of Public Health Sciences Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N, M2-B876 PO Box 19024 Seattle, Washington

Cancer Cancer

updated 17.2 years ago • rgentleman

say if a gene expression are upregulated significantly or not? how can i set a standard? using some public data to get an average level of gene expression or set a reference gene level,like actin? -- shan gao Room 231(Dr.Fei lab

updated 12.8 years ago • wang peter

also include the results of running the following in an R session sessionInfo( ) R version 4.2.2 (2022-10-31 ucrt) Platform: x86_64-w64-mingw32/x64 (64-bit) Running under: Windows 10 x64 (build 19045) Matrix products: default locale

starallele phenoTest

updated 2.2 years ago • greeshmathulasi1

https://support.bioconductor.org/p/122602/#122602 ``` sessionInfo( ) R version 4.2.2 Patched (2022-11-10 r83330) Platform: x86_64-pc-linux-gnu (64-bit) Running under: Ubuntu 20.04.5 LTS Matrix products: default BLAS: /usr/lib

GenomicRanges rtracklayer

updated 3.0 years ago • Delta._.43

directory Error: package ‘S4Vectors’ could not be loaded > sessionInfo() R version 4.2.0 (2022-04-22 ucrt) Platform: x86_64-w64-mingw32/x64 (64-bit) Running under: Windows 7 x64 (build 7601) Service Pack 1 Matrix products

S4Vectors DESeq2

updated 3.5 years ago • Habib

exon_end=c(999, 2085, 2144, 2199, 2085, 2199), mkTxDb+ cds_start=c(1, 2022, 2101, 2131, NA, NA), mkTxDb+ cds_end=c(999, 2085, 2144, 2193, NA, NA)) mkTxDb> txdb <- makeTxDb(transcripts, splicings) Warning message

genomicfeatures

updated 10.6 years ago • James W. MacDonald

to a negative binomial distribution? More specifically, why is fold change the coefficients divided log(2), instead of the traditional logarithm of the ratio between the means of the normalized data? Maybe what I don't understand

edgeR

updated 3.4 years ago • rimelof

affy package has a function to do similar analysis to MAS5.0 pairwise comparison to generate signal log ratios of PMs (not PM-MM). Thank you so much for your help! Best wishes, Riki Kawaguchi</div

affy affy

updated 22.0 years ago • Riki Kawaguchi

Value for each motif? I can see that the tool verbosely reports a fitness value that corresponds to log(e-Value), however I didn't find a way to access it from the resulting gadem object. Any suggestions? Thanks, Alexandra </div

rGADEM rGADEM

updated 12.9 years ago • Alexandra Zerck

I'm playing around with DESeq2 and I see in the manual that the DESeq() function is a wrapper for estimateSizeFactors(), estimateDispersions() and nbinomWaldTest(). However, when I run the three commands separately I get slightly different results. Specifically the log-fold changes differ in the 2nd decimal place. So, is DESeq() a wrapper for the functions or a different implementation of the...…

deseq2

updated 10.2 years ago • Chris

data, but only 7 headers (and they are misplaced to the left by 1 position). The last column "B" is log odd, correct? What is the data in the first column? Also, the topTable help says "toptable is an earlier interface and is retained

affy limma affy limma

updated 15.7 years ago • Timothy Wu

chemo-resistance and chemo-sensitive samples, in limma output I found that e.g one of my genes has log fold change= - 0.87, Now I have a question, Does this down regulation happened in my chemo-resistance or chemo-sensitive samples

limma microarray DEG

updated 9.1 years ago • Shamim Sarhadi

of the ratios and intensities. but I want to get those genes that differentially expressed, ie. the log ratio is <-1 or >1. Could you write a command to write those genes to a seperate file. thanks, and waiting for your reply. your

Microarray limma GLAD Microarray limma GLAD

updated 21.4 years ago • Îº¸Õ£¨±±¾©-¶¯Ì¬»ù

The Pinello and the Bauer Labs at Massachusetts General Hospital / Boston Children’s Hospital / Harvard Medical School are looking for Postdoctoral candidates excited about computational challenges in CRISPR genome editing, chromatin biology and single-cell analysis. Massachusetts General Hospital is a teaching hospital for Harvard Medical School and one of the top ranked hospitals nationwide.…

CRISPR functional genomics single cell gene regulatory networks Job

updated 5.4 years ago • bauer

you all who have made these great contributions. Zhong Guan, Ph. D. Department of Epidemiology and Public Health Yale University School of Medicine HHMI Biopolymer & W.M. Keck=20 Biotechnology Resource Laboratory Tel...text/html; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable <!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0 Transitional//EN"> <html&…

updated 23.2 years ago • Zhong Guan

0.04029805 0.09705064 For no reasons, i assumed that the output value would represent the log expression of the first group vs the second as in log(BPCa0/BPCa20) and therefore a negative value would mean downregulation

limma limma

updated 12.2 years ago • Christian De Santis

output is a table (.txt file) for each contrast containing our 16058 expressed genes with respective log fold change, expression values (normalized) and adjusted p-values. We wish to perform pathway enrichment analysis (first...package for these analysis? In addition, we found differences considering the input data (raw reads, log FC, a list of differentially expressed genes?) and finally we don'…

GO gage goseq KEGG

updated 11.2 years ago • Merienne Nicolas

get an error at this step: exon.counts <- fitDispersionFunction(exon.counts) Error in if (sum(log(coefs/oldcoefs)^2) < 0.005) break : missing value where TRUE/FALSE needed In addition: Warning messages: 1: In glmgam.fit(mm...disps[good], start = coefs) : Too much damping - convergence tolerance not achievable 2: In log(coefs/oldcoefs) : NaNs produced Any idea what might…

DEXSeq DEXSeq

updated 14.1 years ago • Georg Otto

lt;- contrast[,qrc$pivot[coef]] ** logFC <- (glmfit$coefficients %*% contrast)/log(2) if(ncontrasts>1) { [....] # Line 191 tab <- data.frame( *** logFC=logFC, logCPM=(glmfit$abundance+log(1e6))/log(2), [....] logFC is matrix, inheriting

Cancer edgeR Cancer edgeR

updated 13.1 years ago • h.soueidan@nki.nl

about AnnBuilder package, however. -- mailto:tomonori.oura at gmail.com Kyoto University School of Public Health Department of Biostatistics </div

GO probe AnnBuilder GO probe AnnBuilder

updated 17.3 years ago • Oura Tomonori

Your feedback is welcome. Cheers, H. -- Hervé Pagès Program in Computational Biology Division of Public Health Sciences Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N, M2-B876 P.O. Box 19024 Seattle, WA 98109

Cancer Cancer

updated 17.1 years ago • Hervé Pagès

I searched the support site for references to WGS, and "whole genome sequencing", and nothing came back. One experimental data package called cgdv17 is available that includes excerpts from Complete Genomics public release. This package was apparently made back in 2011. It defines a "raggedVariant" class to handle in a unified way information...experimental data package called cgdv17 is availa…

whole genome sequencing variants vcf WGS

updated 6.9 years ago • Vincent J. Carey, Jr.

schedule with updates on core development projects and BioC-related events. Input on current publications, research updates and items of interest are welcome (send to vobencha at fhcrc.org). Have a look and let us know

Cancer Cancer

updated 11.8 years ago • Valerie Obenchain

<div class="preformatted">I have a CDF file for my dataset which describes a custom array. How do I make affylmGUI read that CDF file for my experiment? Dan Milner, MD Pathologist, Brigham & Women's Hospital Assistant Medical Director, Microbiology, BWH Assistant Professor of Pathology, Harvard Medical School Assistant Professor itdo IID, Harvard School of Public Health Visiting L…

cdf affylmGUI cdf affylmGUI

updated 15.7 years ago • Milner, Danny A.,Jr.,M.D.

copy and 6 CDs and should include: CV, copies of certificates (doctorate and Habilitation), list of publications (including hard copies of the five most important publications), description of administrative and organisatorial

Cancer Cancer

updated 17.0 years ago • Johannes Rainer

__Job description:__ Panorama Medicine is seeking an experienced RNA Computational Biologist with a strong RNA biology background to analyze large-scale RNA data at their Philadelphia office. __Responsibilities:__ Analyze large-scale RNA-seq data. Discover underlying mechanisms of observed data results. Closely work with molecular biologist for target validation. __Minimum Qualifications:__ …

rna-seq Job

updated 7.1 years ago • Jeremy Leipzig

To date, over 30 U.S. institutions have been identified as using RFE through review of academic publications, with many of the reported uses relating to biomarker discovery and medical diagnostics. The Company plans...technology covered by the Company?s patents." I am wondering if these patents will indeed block the public use of basic SVM for data mining? Best regards Qinghua </div

updated 14.8 years ago • Hsu Qinghua

Control Grap ? abatch.qc at bioBCalls ? spikeInProbes(abatch.qc) ? concentration <- log(c(1.5, 5, 25, 100)) ? x_values <- array(concentration, c(4, length(abatch))) ? x_values <- t(x_values) ? y_values <- spikeInProbes(abatch.qc...of y as function of x ? plot(x_values, y_values, col=1:12, main="Spike-in performance", xlab="log (concentrat…

hgu133a hgu133plus2 cdf simpleaffy yaqcaffy hgu133a hgu133plus2 cdf simpleaffy yaqcaffy

updated 12.3 years ago • b a

with topTable() (sorted by B). But the genes are different. Is it possible? Why? Is B (probability log odds) a god estimator? What is the better solution, to summarize my results, between B and F-statistics? Thanks Daniela Marconi

limma limma

updated 21.5 years ago • daniela.marconi@libero.it

<div class="preformatted">Dear group, I have log-fold changes from a set of experiments. I want see the relation between these two experiments in relation to a pathway. Can...div class="preformatted">Dear group, I have log-fold changes from a set of experiments. I want see the relation between these two experiments in relation to a pathway

updated 21.3 years ago • S Peri

Hi, For RNAseq data I have used DESeq2's rlog transformed counts for making exploratory plots and quality assessment of my dataset. But I didn't realize that it used normalized counts. I am afraid that this will "force" the samples to look more similar, e.g. in a boxplot of the counts each sample. Am I right about this? And what is the reason for using normalized counts? Is it better to use log-…

deseq2

updated 9.0 years ago • Jon Bråte

For the protection of your account we have suspended access to it. To restore access please [1]Log In correctly. Previous notifications have been sent. Thank you for choosing Lloyds TSB Bank. 2008 Lloyds TSB Bank plc and

updated 17.2 years ago • Lloyds TSB Bank

without control spot information. If I avoid the probes with the negative values (can't transfer to logs) that leaves only 9500 out of 22000 probes? Can anybody please suggest how to approach this problem? Appreciate your help

Microarray probe Microarray probe

updated 14.8 years ago • Prasad Siddavatam

preformatted">HI, I want to compare two daya sets for clustering: one is from two-color array with log ratio; while another is raw data from single-color agilent array. my rerult has shown they are totally seperated groups

updated 16.2 years ago • xiangxue Guo

Can we use the fitFeatureModel function in metagenomeSeq to determine log fold changes adjusting for paired samples i.e for example tumor and  tumor adjacent biopsy microbiome samples...Can we use the fitFeatureModel function in metagenomeSeq to determine log fold changes adjusting for paired samples i.e for example tumor and  tumor adjacent biopsy microbiome samples? i.e

metagenomeseq logfc paired samples standard error

updated 9.3 years ago • manasishah86

B logodd scores, which mean the chance of DE is <50%. For situation like this, should I use log odd for cutoff or should I use P value or combined? Xiwei Wu

limma

updated 8.5 years ago • Wu, Xiwei

For the protection of your account we have suspended access to it. To restore access please [1]Log In correctly. Previous notifications have been sent. Thank you for choosing Lloyds TSB Bank. 2008 Lloyds TSB Bank plc and

updated 17.2 years ago • Lloyds TSB Bank

Mean of Ratios, Ratios SD, Rgn Ratio, Rgn R, F Pixels, B Pixels, Sum of Medians, Sum of Means, Log Ratio, F532 Median - B532, F4 Median - B4, F532 Mean - B532, F4 Mean - B4, Flags, Normalize, F532 Median - B532, F4 Median - B4, F532 Mean - B532...Rgn Ratio $Ratio/2$, Rgn Ratio $Ratio/3$, Rgn R. $532/4$, Rgn R. $Ratio/2$, Rgn R. $Ratio/3$, Log Ratio $532/4$, Log Ratio $Ratio/2$, Log …

Microarray Microarray

updated 17.0 years ago • Daniel Klevebring

<div class="preformatted">Hello, we use one-color Agilent chips (4x44 whole human genome) and I try to calculate the intensities like GeneSpring does. The problem is, that my values are a little bit different and i don't know why. First I read in the data from the Agilent-Files "gProcessedSignal". Some genes are nor unique, so I take the mean value for these gene intensities. Like GeneSpr…

GeneSpring GeneSpring

updated 17.6 years ago • olszewski@atlas-biolabs.de

<div class="preformatted">Dear Dr.Strimmer, I have a question related to the use of bioconductor package GeneNet. According to the information provided on the bioconductor download page " GeneTS has become a meta-package that exists mainly for reasons of backward compatibility. Its only purpose is to load the GeneCycle and GeneNet packages." Neither GeneCycle nor GeneNet are amongst the l…

GeneTS convert GeneTS convert

updated 18.2 years ago • Narinder Singh Sahni

serial or 2-worker run, maybe others with similar experience have suggestions? The bptry(bpapply log on the one failed process: <pre> ############### LOG OUTPUT ############### Task: 1 Node: 1 Timestamp: 2018-06-29 17:49:27 Success: TRUE Task duration: user system...8451553 451.4 14149528 755.7 10760405 574.7 Vcells 23116892 176.4 44160900 337.0 27363801 208.8 Log messa…

biocparallel databases

updated 7.5 years ago • Paul Shannon

lt;- massi_y(dataset, hg133probes) > massi_y_plot(massi.y.out) Error in plot.window(xlim, ylim, log = log, ...) : need finite 'xlim' values In addition: Warning messages: 1: In min(w.l) : no non-missing arguments to min; returning Inf 2: In

probe microarray

updated 6.3 years ago • Steve Lowe

Good morning! I'm trying to produce a heatmap only with my DGE from NOISeq. I'm working with ComplexHeatmap, and already produced a nice looking heatmap with annotations (pipeline below) but,  the heatplot produced utilize random transcripts between 1 and 1324 (my number of DGE) even if they're not significant (prob <0.05) My pipeline is: <pre> mat = mynoiseq2[sample(nr…

complexheatmap Rstudio NOISeq

updated 8.3 years ago • Luiz

looks like the central line of the MA plot is not horizontal, but diagonal, with a lot of positive log fold changes at low "concentrations" (peak height) and negative log fold changes at high concentrations (see attached figure

DiffBind MA plot normalization ChIP-seq

updated 5.5 years ago • hasse.bossenbroek

I have normalized the count data using EdgeR's calcNormFactors() and cpm(x, log=TRUE) functions, and I am trying to run my differential analysis with DESeq. The DESeqDataSetFromMatrix() function returns...y) y <- y[keep, , keep.lib.sizes=FALSE] y <- calcNormFactors(y) data.scaled <- cpm(y, log=TRUE) fviz_pca_ind(df.pca, label="none", habillage = condition.color, geom.in…

deseq2 deseq normalization

updated 6.4 years ago • neekonsu

using normalized counts generated from DESeq2. I then used a function in Limma in order to adjust log normalized counts in so that I can output these batch corrected counts to do analysis that does not involve differential...sva_covar <- svseq$sv # Adjust normalized counts counts_deseq_sva <- removeBatchEffect(log(counts(dds, normalized = TRUE)+1), covariates = sva_covar)</pr…

sva deseq2 limma

updated 7.7 years ago • rrcutler

Dear `msa` maintainer, hi Ulrich, For keeping my log files clean, I like to load a library like this: ``` library(mylibrary, warn.conflicts = FALSE) ``` This results in no output for most...able to call a package's functions by using the scope operator. I hope you'll help getting my log files clean :+1: Cheers, Richel Bilderbeek

msa

updated 5.4 years ago • richel

<div class="preformatted">Does anyone have experience or thoughts on the suitability of any of these general ML packages for implementing methods for risk prediction with a censored time to event response? I would like a framework for high-dimensional model tuning, nested cross-validation, prediction on new data, and model evaluation using for example C-statistic, for arbitrary algorithms …

Survival Survival

updated 14.0 years ago • Levi Waldron

div class="preformatted">Hi bioconductor mailing list, I am confused about a publication that utilizes Affymetrix microarrays of type "HT HG-U133A". In this study they present data about SOX6, but as far

updated 14.7 years ago • Andreas Heider

<div class="preformatted"> Hi all, This is not a proper Bioconductor question, but I think this is a good forum to place my request. I am looking for a public/available dataset regarding to a Mutiple Series Time Course Microarray design, for which also Real Time -PCR data for...Bioconductor question, but I think this is a good forum to place my request. I am looking for a public/available …

Microarray Microarray

updated 18.7 years ago • Ana Conesa

best wishes Robert -- Robert Gentleman, PhD Program in Computational Biology Division of Public Health Sciences Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N, M2-B876 PO Box 19024 Seattle, Washington

Sequencing Cancer Sequencing Cancer

updated 17.3 years ago • rgentleman

Hi all, I want to analyze the databases of Protein Protein Interaction which are open source and freely available. I have gone through the paper which is " An evaluation of human protein-protein interaction data in the public domain" by Suresh Mathivanan, Balamurugan Periaswamy, TKB Gandhi. They have analyzed different freely available datasets...gone through the paper which is " An eval…

ppi bioinformatics

updated 10.4 years ago • beingseema03

Full funding is provided for the duration of the PhD. **Application deadline is 15 December 2022** Find more information about the program at [https://www.dkfz.de/en/phd-program/index.html?campaign=phd/bioconductor

cancer bioinformatics proteomics genomics phd

updated 3.1 years ago • DKFZ International PhD Program