Bioconductor Forum

1] 6 [1] "The ensemble mode was disabled." [1] "EGSEA analysis has started" [1] "Log fold changes are estimated using limma package ... " [1] "EGSEA is running on the provided data and c2 gene sets" Running PLAGE...1] 7 [1] "The ensemble mode was disabled." [1] "EGSEA analysis has started" [1] "Log fold changes are estimated using limma package ... " […

egsea

updated 8.7 years ago • irizarnaunk

<div class="preformatted">Dear Wei, In principle the biomaRt package can be used with any BioMart database. However the HapMap BioMart suite is an old version which has no webservice capabilities and the HapMap project has also not made a public MySQL access to their database available yet. As soon as the HapMap project updates their BioMart suite to a more recent version or makes public …

HapMap biomaRt HapMap biomaRt

updated 18.9 years ago • Steffen Durinck

of MPRA dataset using DESeq2. We chose DESeq2 based on its successful application in Abell et al., 2022 MPRA paper, which used a similar haplotype-based MPRA design. I expected that with some minor adjustments, their approach

Bioconductor

updated 12 weeks ago • Rita

the results of running the following in an R session sessionInfo( ) ```R version 4.2.2 (2022-10-31) Platform: aarch64-apple-darwin20 (64-bit) Running under: macOS Monterey 12.5 Matrix products: default LAPACK: /Library

Salmon tximport RNAseq EdgeR

updated 3.1 years ago • Jenni

CRAN: https://cran.rstudio.com/ Bioconductor version 3.16 (BiocManager 1.30.19), R 4.2.2 (2022-10-31 ucrt) Installing package(s) 'org.Mm.eg.db' installing the source package ‘org.Mm.eg.db’ trying URL 'https://bioconductor.org

Bioconductor

updated 3.0 years ago • Anastasia

<div class="preformatted">Hi Steffen Just wondering - has there been any change on this since your post in early 2007 - i.e. do HapMap now have webservice or public MySQL capabilities? Best wishes Richard. Steffen Durinck wrote: > Dear Wei, > > In principle the biomaRt package can be used with any BioMart database. > However the HapMap BioMart suite is an old…

HapMap biomaRt HapMap biomaRt

updated 17.7 years ago • Richard Pearson

BioAge Labs is a clinical-stage venture-backed biotechnology company headquartered in Richmond, CA. We’ve built a systems biology platform to map out the key molecular pathways that impact healthy human aging, based on proprietary human aging cohorts that have blood samples collected up to 45 years ago with participant-omics data that is tied to detailed medical follow-up records over their lifes…

BioAge ComputationalBiology JobPosting

updated 4.6 years ago • jamie

Tennis Court Road, Cambridge CB2 1QP Tel: 01223 333331 and MRC Biostatistics Unit Institute of Public Health, Robinson Way, Cambridge CB2 0SR Tel: 01223 767408 Email: kak28 at cam.ac.uk </div

updated 18.3 years ago • Krys Kelly

Cancer Science, M. D. Anderson Cancer Center in Houston. https://2xrecruit.kenexa.com/kr/cc/jsp/public/EmailJobDetail.jsf?npi=1 482FDE25A0936D396E9938B7C9A0C0C&rand=743A04605C79A792408718D24667EE8B9 D39D8B0C75443E40E055B9DCAE94345

Cancer Cancer

updated 12.4 years ago • Zhang,Jianhua

Hello, I have a simple question. I have 2 public data sets and I want to use both of them with MNN correction for certain analyses. One of the data sets has raw counts...Hello, I have a simple question. I have 2 public data sets and I want to use both of them with MNN correction for certain analyses. One of the data sets has raw counts, which

scRNA-Seq scater scran rna-seq MNN

updated 6.2 years ago • hamza_karakurt

kcdf = "Gaussian" if we have expression values that are continuous such as log-CPMs, log-RPKMs or log-TPMs, kcdf = "Poisson" on integer counts. kcdf = "Poisson", # Minimum gene set size min.sz = 15, # Maximum gene set

ssgsea GSVA biotype proteincoding msigdb

updated 2.1 years ago • snijesh

whether the `lfc` argument and corresponding output column prefixed with `logFC` was log2 or natural log. I assume that it is base 2 as the `limma` output. Thanks in advance! Chris

scran

updated 6.6 years ago • Chris Conley

the BioC 2.0 and 2.4 results from gcrma are not that large: over 48 arrays the ratio new/old of the log-intensity values is 1.001 +/- 0.020, and the ratio of the intensity values is 1.007 +/- 0.090. In another set of arrays, of the RGU34A...the BioC 2.0 and 2.4 results from gcrma is much larger: over 8 arrays the ratio new/old of the log-intensity values is 1.05 +/- 0.16, and the ratio of the in…

Microarray Normalization GO hgu133plus2 rgu34a probe gcrma Microarray Normalization GO

updated 16.4 years ago • Rullmann, J.A.C. Ton

to go for roast I have to use the fit again, but I don't know how to get the treat 1.5 FC in there nor the > 8 RPKM filter. Can anyone suggest a better way to do this? <pre> # ROAST roast_res <- roast(y,index=geneSet,design=design

roast edgeR glmtreat

updated 9.4 years ago • b.nota

fit) topTable(fit, coef=8:12) ``` However, the code from the user guide does not tell me the log fold changes of those proteins. **Thus, I wonder if it is correct to apply the following contrast to my design:** ```r contrast &lt...Treatment_4 + Treatment_5)/5 - CNTR, levels = colnames(design) ) ``` **and then extract log fold changes from:** ```r fit <- lmFit(proteins,…

limma

updated 22 months ago • dl17032000

for gene-wise KCDF estimation: Poisson and Guassian To use the Gaussian kernel, count data must be log-transformed (for example log2 count per million or log2 read per kilo-base per million). For the Poisson Kernel, log transformation

gsva gene set variation analysis normalization transformation rna-seq

updated 7.0 years ago • rached

last vignette, the example on pages 18-19 shows a PCA plot of the samples, obtained with regularized log transformed data (rld). But in the plotPCA R documentation, it is written to use a SummarizedExperiment with transformed...1 = pathology (patients vs control cases) and axis 2 = unknown factor - when transformed with r-log (rld), axis 1 = unknown factor and axis 2 = pathology - when …

DESeq2 DESeq2

updated 12.2 years ago • amandine.fournier@chu-lyon.fr

xlab", "ylab", "cex.lab", "col.lab")]) 7: bxp(z, width, varwidth = varwidth, notch = notch, log = log, border = border, col = col, pars = pars, outline = outline, horizontal = horizontal, add = add, at = at) 6: boxplot.default(data.frame

affy affy

updated 21.0 years ago • Paul Boutros

nbsp;   "p.value"     "treat.lfc" \` >volcanoplot(tfit,coef=1) >plot(tfit\[,6\],-log(tfit\[,10\],10),coef=1, xlab="__log2(Fold-Change)__", ylab="__-log10(P.Value)__",main="Volcano plot",cex=0.1,pch=19) >abline(v=c(-1,1),col="blue...gt;abline(h=-log(0.05,10),col="red")   Thanks in advance

Volcano plot Parameters

updated 8.3 years ago • Sanches

Sequin mixes A and B. When I try to make a ROC plot using the following parameters: - Expected log fold change - 1 minus P-value of measurement - TP/FP label of measurement plotROC collapses all the curves, each one representing...plot - Illumina' # Sequin names seqs <- row.names(exp_gene_sequins) # Expected log fold ratio <- exp_gene_sequins$Int_Log2_Fold…

anaquin plotroc

updated 6.4 years ago • William.Glynn

preformatted">|transformList| is what you are looking for: |tl <- transformList(c("FL1-H","FL2-H"), log) colnames(tl) data(GvHD) transform(GvHD[[1]], tl)| Mike Jiang On 11/19/2013 01:00 PM, Liu, Hongye wrote: > Dear Dr. Jiang, > > How are you...input backtick-ed parameter names into the function. For example, I > can't do transform( ,"FL1-H" = log("FL1-H"…

flowCore flowCore

updated 12.1 years ago • Jiang, Mike

Embedded in the Boston Children’s Hospital / Harvard Medical School research community, the Sr. Bioinformatics Scientist will collaborate with pediatric researchers on a variety of projects ranging from translational and clinical research to basic science studies. Members of our community have varying levels of bioinformatics expertise and work on diverse disease areas including rare pediatric di…

JobPosting

updated 4.8 years ago • shira.rockowitz

## Research Associate (Bioinformatician) (Fixed Term) __Apply via[ http://www.jobs.cam.ac.uk/job/12962/](http://www.jobs.cam.ac.uk/job/12962/)__ --- Applications are invited for the post of a Post-doctoral Bioinformatician to work on a collaborative translational research project between the groups of Dr Matthias Zilbauer (Department of Paediatrics at the University of Cambridge, UK), Dr. Paul…

postdoc bioinformatician biomedical informatics bioinformatician job job Job

updated 8.9 years ago • kraiczy

I am trying to merge GEo data from different authors, most are in raw counts and I would convert to log CPM, but one dataset is in Normalized count (DESeq Normalization). Which package can I use to undo the normalization or convert

DESeq2 Normalization RNASeq

updated 3.3 years ago • adeizadavid

methylated genes. If I used the pvals as the weights, is it reasonable? I do like this. w<-log(pvals(mldat),0.01) fit1 <- lmFit(exprs(mldat.norm), dm,weights=w) Thanks. </div

limma methylumi limma methylumi

updated 15.4 years ago • Jinyan Huang

any package which works similarly as SPIA (Signaling Pathway Impact Analysis ) package? I have log fold change values for a list of genes. Now, I want to use them for different pathway enrichment analyses to find out which

SPIA pathway enrichment analysis overrepresentation

updated 6.8 years ago • asifgeb

Greetings. We were interested in determining unique genes in the lower canopy of legumes. We had an RNA-Seq data of Cowpea and Soybean. I am trying to analyze the Cowpea data at a SINGLE time point (flowering...Greetings. We were interested in determining unique genes in the lower canopy of legumes. We had an RNA-Seq data of Cowpea and Soybean. I am trying to analyze the Cowpea data at a SINGLE…

DESeq2

updated 4.1 years ago • tarun2

div class="preformatted">The publication for CAMERA (http://nar.oxfordjournals.org/content/earl y/2012/05/24/nar.gks461.full) mentions using the average

GO limma CAMERA GO limma CAMERA

updated 13.3 years ago • Simon de Bernard

for labeled mass spectrometry counts. We will also greatly appreciated it if you could send us some publications in this area. Thank you so much

deseq2

updated 8.6 years ago • maduanduan8

enrichment results by means of the `` enrichMap `` function (for an example see the original publication, Figure 1 http://pubs.rsc.org/en/content/articlepdf/2016/mb/c5mb00663e). I am wondering though what the connections

reactomepa

updated 8.5 years ago • juls

div class="preformatted">Hi, I did analysis of some public available microarray data sets (available as .cel files), then mapped the affymatrix probe IDs to EnsEMBL ID by EnsMart

Microarray probe Microarray probe

updated 20.5 years ago • Wuming Gong

variety of biological data on molecular and genetic pathways, and produces interpretable graphs with publication quality. Pathview web server provides a user friendly access. Please try it, and let us know if you have any problem

pathview pathway analysis visualization web server omics data

updated 10.0 years ago • Weijun Luo

Hello Bioconductor,  We have added DOI's for packages on Bioconductor package landing pages. The DOI will get generated automatically when a package is accepted to Bioconductor. This is the recommended reference to use for publication/citations/etc.  The DOI link should automatically redirect to the current release version of a package (or...when a package is accepted to Biocon…

DOI doi packages citation publication News

updated 8.2 years ago • shepherl

A recent publication in PLoS Biology documents sample specific biases in differential expression analyses related to gene length

RNASeq tximport

updated 6.1 years ago • abf

data related to cardiovascular disorders, especially arteriosclerosis. We expect this to lead to publications in high profile medical journals. Many projects in the group relate to the interplay between genetic and environmental...an interest and basic understanding of molecular biology. We expect all applicants to have a good publication record; this will be one of the most important criteria fo…

Genetics Genetics

updated 16.2 years ago • Christoph Preuss

Assist faculty and staff with large-scale mining and analysis of diverse private and public databases. - Analyze data using established and novel workflows developed by internal and external groups. - Work within...years). - Experience (1-3 years) with R and python or perl is required. - Working knowledge of public biological databases (NCBI, ENCODE, ENSEMBL, TCGA, etc.). - Experience m…

job bioinformatics research scientist analyst Job

updated 5.8 years ago • deanpett

Hello Everyone! I'm recently tring to install the Packages EnsDb.Hsapiens.v75 on the CentOS 7.9 HPC system of our lab. So I try to install it in a conda env R4.1.3 and R4.2 by using: ```r BiocManager::install('EnsDb.Hsapiens.v75') ``` But it turns out error like this: ```r Bioconductor version 3.14 (BiocManager 1.30.18), R 4.1.3 (2022-03-10) Installing package(s) 'EnsDb.Hsapiens.v75' …

EnsDb.Hsapiens.v75

updated 3.1 years ago • hjh811638667

I am converting murine gene lists to human genes using the code below from https://www.r-bloggers.com/2016/10/converting-mouse-to-human-gene-names-with-biomart-package/ ```r convertMouseGeneList <- function(x){ require("biomaRt") human = useMart("ensembl", dataset = "hsapiens_gene_ensembl") mouse = useMart("ensembl", dataset = "mmusculus_gene_ensembl") genesV2 = getLDS(attributes…

biomaRt RNASeqData R

updated 3.7 years ago • Dina

CRAN: https://cloud.r-project.org Bioconductor version 3.14 (BiocManager 1.30.16), R 4.1.3 (2022-03-10) Installing package(s) 'edgeR' also installing the dependencies ‘limma’, ‘locfit’ probando la URL 'https://bioconductor.org...had non-zero exit status ``` gretings! my session info is ``` > sessionInfo() R version 4.1.3 (2022-03-10) Platform: x86_64-pc-linux-gnu (64-bit) Running unde…

BiocManager edgeR

updated 3.8 years ago • alam

xxx/chunks/chunk_000003/logs/progress.log 2023-09-25 17:53:35 DEBUG::tools.R/processChunks: starting chunkid= 4 ; see logfile= ~/Downloads/Pilot/analysis...xxx/chunks/chunk_000004/logs/progress.log 2023-09-25 17:53:44 DEBUG::tools.R/processChunks: starting chunkid= 5 ; see logfile= ~/Downloads/Pilot/analysis...xxx/chunks/chunk_000005/logs/progress.log 2023-09-25 17:53:53 DEBUG::tools.R/processChu…

HTSeqGenie

updated 2.3 years ago • zh9118

Hi! I conducted DGE analysis between 2 groups of cell lines MYCN amplified vs MYCN non amplified. Cell lines in the MYCN non amplified group had these FPKM values for MYCN gene: 5.182582, 3.104376, 4.962478 Cell lines in the MYCN amplified group had these FPKM values for the MYCN gene: 101.2204, 301.8182 , 280.6712 Now visually there is a marked difference between these two groups and s…

limmaGUI edgeR limma

updated 21 months ago • Simran

I expect G=3 as a best result of number of Gaussians to consider, but I need a number (I guess the log likelihood) that describes the significance of this case. Many use MCLUST (R package) for modeling data as a Gaussian finite...alternative method could be to perform a FOR cycle in which I change the G value and I compare the log likelihood values.. ---------- Have you advices? What …

software error microarray probe annotation

updated 6.9 years ago • travascio.andrea91

on the array). If you only have one array, you have to rank the genes simply according to their log-ratios. Would it help to have functionality in 'toptable' to rank genes on log-ratio alone when there is only one array? Gordon

limma limma

updated 22.4 years ago • Gordon Smyth

numeric 'envir' arg not of length one I have follwed the code almost exactly but defined log="x". Here is the code I have entered: print(xyplot( -log10( pval ) ~ log2FoldChange, + res$baseMean, + log="x", pch=20, cex=.2, + col=ifelse( res$padj

RNASeq DESeq RNASeq DESeq

updated 13.8 years ago • Melissa.Martin@lshtm.ac.uk

set.seed(353567) ddsRaw <- makeExampleDESeqDataSet(n=1000, m=40) gm <- exp(rowMeans(log(counts(ddsRaw)))) dds <- estimateSizeFactors(ddsRaw, geoMeans=gm) ddsSubset <- estimateSizeFactors(ddsRaw[, 10:20], geoMeans...dependent on the reference geometric means. ```r if (incomingGeoMeans) { sf <- sf/exp(mean(log(sf))) } ``` Thanks

size factors deseq2

updated 5.4 years ago • Megatron

how can i map the position of each gene on human chromosomes and if possible plot signal intensities, log and raw. This is my first stab at this, so kindly pardon my ignorance on this issue. Thanks, Hrishi </div

updated 20.2 years ago • hrishikesh deshmukh

on the image ( I got 700 on the X and the Y) ? How is this scaling done ? 2. How do i turn off the log scaling? Thanks Shyam </div

updated 22.9 years ago • Sundaram, Shyam NIH/CIT

my data using RPM based normalization and looking to check the differential expression and log fold change. is there any methods so that i can test with more than one statistics to strengthen my analysis. Thanks in Advance

deseq2 differential expression

updated 8.6 years ago • Bio_Ram

on the log2FC values from these comparisons. My question is whether I should use the shrunken log fold changes from "lfcShrink()" function or use the raw log2FC values

deseq2 gsea rnaseq gene espression

updated 6.9 years ago • bmreilly

a way to not loose the iD information after doing y<-calcNormFactors(y) and logCPM<-cpm(y, log=TRUE, prior.count=2)? I really need to cross information from logCPM with other data... Thanks in advance, Patrícia &nbsp

edgeR

updated 8.5 years ago • abrantes.patricia

div class="preformatted"> Hello, Does anyone know of a decent compiler for R either public domain or commercial that one can use to trace values in a program. I can use cat and trace ..etc but it would be nice to have

updated 17.3 years ago • Ruppert Valentino

would greatly appreciate it if you can share with my an example of the marioni dataset used in this publication below I need to add the variables (mylength, mygc, mybiotype, mychromosome)! Anyhelp will be much appreciated&nbsp

R noiseq data.frame

updated 7.9 years ago • aokoro

Lang Chen Research Assistant Department of Biostatistics Section on Statistical Genetics Ryals Public Health Building, Suite 343A University of Alabama at Birmingham 1530 3rd Ave S Birmingham, Alabama 35294 Tel 205-9757772

updated 22.6 years ago • Lang Chen

that? Thanks, Alice Arcury-Quandt Research Assistant Department of Epidemiology Division of Public Health Sciences Wake Forest University School of Medicine Winston-Salem, NC 27157 [[alternative HTML version deleted

Annotation Annotation

updated 15.4 years ago • Alice E. Arcury-Quandt

Hi, I have been annotating VCF files with VEP. utils::download.file("https://i12g-gagneurweb.in.tum.de/public/bugreports/bioc_variantAnnotation/example_no_anno.vcf.gz", "example_no_anno.vcf.gz") utils::download.file("https...been annotating VCF files with VEP. utils::download.file("https://i12g-gagneurweb.in.tum.de/public/bugreports/bioc_variantAnnotation/example_no_anno…

software error VariantAnnotation ensemblVEP

updated 6.8 years ago • mumichae

main source of variability among my samples R/N/Rep.Class.Unk : status of my samples (responder/nor responding/unknown status) PD/PR/SD : Experimentally observed variable. First, I want to get the gene differentially expressed

Microarray Microarray

updated 14.0 years ago • Guillaume Meurice

why this approach should introduce some biases, but of course I'm not an expert of tximport/Deseq2 (nor of CoxPH by the way...) so I have some paranoia. Thanks a lot in advance

deseq2 vst cox-regression Salmon Tximport

updated 6.8 years ago • filippo.martignano

this is as of Fri Sep 16 09:17:53 UTC 2011) I cannot resolve this domain from Holland, nor from California. This seems to happen more often; see also e.g. https://stat.ethz.ch/pipermail/bioconductor/2010-January

Cancer PING Cancer PING

updated 14.3 years ago • Philip Lijnzaad

I disagree with this statement. The htmlpage() function isn't designed >to be completely flexible, nor IMO should it be. Well, I won't argue with you over this. It is your software and your design. How about htmlpagemoregeneric

updated 16.9 years ago • john seers IFR

that the plots will be of background-subtracted values if background correction has not been done, nor is there anyway to change this behavior within the calls. The other people and myself thought we were looking at raw, non

limma limma

updated 19.7 years ago • Jenny Drnevich