Bioconductor Forum

Hi there, I have a processed microarray dataset (HG-U133A) downloaded from the ArrayExpress. The authors have processed the data using RMA in affy package and only the processed data is available. What I have now is a spreadsheet containing a summary of normalized expression values. I know that for using limma, it is assumed that we have "__eset__" of class "__exprSet__", however, the dataset I …

limma microarray

updated 10.9 years ago • Momeneh Foroutan

2005) 44, 5328-5338. 15807526 ``` BrendaDb returns the reference and PubMed id of some publications associated with the enzyme process (EC or KO code), I have filtered functions to "just" 200 via differential analysis...already exists somewhere. Is there a method/function, within brendaDb or outside, to filter these publications by organism

brendaDb

updated 3.5 years ago • Lluís Revilla Sancho

pc-linux-gnu (64-bit) Running under: Ubuntu 20.04.2 LTS Matrix products: default BLAS: /data/public/R_4.1.0/lib/R/lib/libRblas.so LAPACK: /data/public/R_4.1.0/lib/R/lib/libRlapack.so locale: [1] LC_CTYPE=C.UTF-8 LC_NUMERIC

destiny BiocVersion

updated 4.5 years ago • Yiming

sequencing projects in the area of cancer genomics. In-house generated data as well as selected public domain data sets should be integrated with an already existing large data collection. A strong focus will be the comprehensive...should contact Christian.Haslinger at boehringer-ingelheim.com along with copies of their CV, publication list and names of reference persons. </div

Cancer Cancer

updated 16.5 years ago • Ido M. Tamir

tasks:__ - Developing novel techniques in the field of Statistical Bioinformatics - Scientific publications - Grant writing - Supervision of PhD students - Bioinformatics consulting in support of the Core Facility Bioinformatics...and health care benefits - Child care (conditional on places available) - Job ticket for public transport For further information on the scientifi…

bioinformatician job rnaseq statistics systemsbiology Job

updated 10.7 years ago • Federico Marini

and renders a large variety of biological data onto pathways, and produces interpretable graphs with publication quality. Pathview was quickly adopted and widely used by thousands of scientists worldwide. With a major NSF...building highly quality software, enjoy data analysis Proven research/development experience, publication record is a plus __Education:  __ PhD (or Master + 3 …

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updated 9.3 years ago • Luo Weijun

<div class="preformatted">Hi, Adrian, I'm using your topGO package and really appreciate how powerful and customizable it is with respect to the choice of algorithms and statistical tests. There's just one limitation that I don't really understand, hopefully you or somebody else in the list can shed some light on this. I usually select 'interesting' genes from gene expression experiments…

GO probe topGO GO probe topGO

updated 12.4 years ago • enricoferrero

as the formulae are set straight. following is my best guess Signal = Average of Tukey_Biweight(log(PM-CT)) if MM < PM, CT=MM if MM > PM, CT=PM/exp(proportion) proportion = Average of Tukey_Biweight(log(PM/MM)) (over all pairs on the

cdf cdf

updated 23.2 years ago • Kenny Ye

batch=batch and batch2=location but that didn't work. `toplot<-(removeBatchEffect(cpm(dge,log=TRUE,prior.count=5),batch=batch,batch2=location,design=design)) error: "Partial NA coefficients for 7319 probe(s)"` Then I tried...corfit <- duplicateCorrelation(v,design,block=batch) toplot <- removeBatchEffect(cpm(dge,log=TRUE,prior.count=5), batch=location, design=design,…

limma BatchEffect duplicatecorrelation block batch

updated 5.1 years ago • Katherine

help. Thank you so much. Here is a sessionInfo() output: ``` > sessionInfo() R version 4.2.2 (2022-10-31) Platform: x86_64-conda-linux-gnu (64-bit) Running under: Springdale Open Enterprise Linux 8.4 (Modena) Matrix products

DiffBind

updated 3.0 years ago • narzouni

Homo sapiens - release 39 ] useHub=TRUE: checking for TxDb via 'AnnotationHub' snapshotDate(): 2022-04-21 did not find matching TxDb via 'AnnotationHub' building TxDb with 'GenomicFeatures' package Import genomic features

DESeq2 tximport tximportData tximeta

updated 3.5 years ago • uhlkatie

control.line) && !is.na(control.line) is not TRUE sessionInfo( ) R version 4.2.0 (2022-04-22 ucrt) Platform: x86_64-w64-mingw32/x64 (64-bit) Running under: Windows 10 x64 (build 19042) Matrix products: default locale

ENmix IlluminaHumanMethylationEPICmanifest

updated 3.7 years ago • Daphna

gt; >> this message or the use or disclosure of the information it contains may > >> violate the law and subject the violator to civil or criminal penalties. > >> If you believe you have received this message...gt; > Herv? Pag?s > > > > Program in Computational Biology > > Division of Public H…

Annotation GO Cancer Apis mellifera BSgenome Biostrings Category BSgenome rtracklayer GO

updated 13.8 years ago • Matthew Young

are nested effect interaction (random effect) in statistical model. Looking to my results the log foldchange seems to be wrong to me. Some genes have too high or too low LogFC values such as -14997.66667 with p-adjust 0.02518022

limma RNAseq foldchange

updated 6.8 years ago • susana.amaral.teixeira

Hi, I am analyzing a data set with expression value of genes in the following conditions: cells with and without drug treatment at 3 different temperature(T): Control-T50 x3, Treatment-T53 x3, Control-T53 x3, Treatment-T53 x3, Control-T57 x3, Treatment-T57 x3. I processed the data using this pipeline: raw data > log2 transformation>median normalization for each temperature group (becau…

limma

updated 2.4 years ago • Erin Yu

Dear community, I have been reading the usersguide of limma package in order to get some useful indications about how can I define the Amean's cutoff but after following the indications provided there I got a little bit confused. In fact, in the page 34 of the usersguide it is written: " A histogram of the Amean values and a sigma vs Amean plot may help identify a cutoff below which Amean val…

limma

updated 3.5 years ago • OE

Hello, I'm encountering an odd situation where the effect of stimulation on a gene's expression seems to flip sign after applying limma+voom. We noticed this when the data plotted as log2(cpm+0.01) seemed to have an opposite effect size as the results of lmFit. The gene is pretty highly expressed (log2(CPM) ~ 8) with 140-4000 reads per sample and time point. For comparison, I'm showing below the …

limma limma-voom rnaseq voom

updated 4.3 years ago • taur.vil

I have been using B values to rank genes in order of more likely to less likely (differentially expressed) in LimmaGUI. I am now using Limma, I noticed the default value for the parameter "proportion" (on the function eBayes) is set at 0.01 (expected 1% differentially expressed genes). I didn't pay much attention to this parameter before, because in LimmaGUI you cannot specify it. However, now…

limma limmaGUI limma limmaGUI

updated 19.7 years ago • J.delasHeras@ed.ac.uk

Hi all, I'm a new to arrayQualityMetrics, so hopefully this isn't an obvious question, but I've been getting the error below when I attempt to run arrayQualityMetrics on several GEO files, including: [GDS961](http://www.ncbi.nlm.nih.gov/sites/GDSbrowser?acc=GDS961) and [GDS4012](http://www.ncbi.nlm.nih.gov/sites/GDSbrowser?acc=GDS4012). The error I've received is:

Erro…

arrayqualitymetrics bugs error

updated 11.2 years ago • daugherty_a

I am working with RNA seq data. I would like to compute the residuals with DESeq2 to remove confounding effect in the data before running WGCNA. We computed the residuals by using DESeq2 on our RNA Seq count matrix with this code: fitted.common.scale = t(t(assays(dds)\[\["mu"\]\])/sizeFactors(dds)) counts(dds, normalized=TRUE) - fitted.common.scale WGCNA suggests to log2…

deseq2 residuals wgcna

updated 8.8 years ago • glmazzo

In reference with Vignette, workflow and DESeq2 paper , rlog = log2(qij) =βi0+βij where qij is a parameter proportional to the expected true concentration of fragments for gene i and sample j (see formula below), βi0 is an intercept which does not undergo shrinkage, and βij is the sample-specific effect which is shrunk toward zero based on the dispersion-m…

deseq2

updated 6.8 years ago • surabhijagtap95

Hi Ben, Well, all models are approximate, the real question is, how sensitive are they to deviations from model assumptions which are likely to occur in practice. The two-sample t-test holds up remarkably well under moderate deviations from normality, equal variances etc. On the other hand, the variance test you have used is known to be exceptionally sensitive to its assumptions. You might be am…

Microarray limma Microarray limma

updated 19.7 years ago • Gordon Smyth

BiocManager") BiocManager::install("edgeR") sessionInfo( ) R version 4.2.1 (2022-06-23 ucrt) Platform: x86_64-w64-mingw32/x64 (64-bit) Running under: Windows 10 x64 (build 22000) Matrix products: default locale...CRAN: https://cran.rstudio.com/ Bioconductor version 3.15 (BiocManager 1.30.18), R 4.2.1 (2022-06-23 ucrt) Installing package(s) 'CATALYST' also installing the d…

CATALYST

updated 3.5 years ago • David

div class="preformatted">Hi Maria, You have not told us about the operating system you are using, nor about versions of packages. I have found the source of the problem. For simLL("10554","10486") the problem is that the gene with...gt;> | Head, Program in Computational Biology fax: (206) 667-1319 | >> | Division of Public Health Sciences office: M2-B865 &a…

GO Cancer graph GO Cancer graph

updated 20.7 years ago • rgentleman

import data from different formats, use Excel-like spreadsheet for manipulating your data, create publication-quality reports, generate editable graphics ... and click click to run your favorite models through dialogs. Check

updated 17.3 years ago • sue@xlsolutions-corp.com

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

information on chromosomal location (i.e. base pairs from the telomere) is available. However, other public databases like Golden Path offer start and end positions for each probeset on the array. What is the reason for this

hgu133a AnnBuilder safe hgu133a AnnBuilder safe

updated 19.5 years ago • Hilmar Berger

Package developers, On June 6 we will transition to our new 'package tracker' on github. The new system will enable a more public review process where community members (not just the assigned reviewer) can give technical and scientific input during...6 we will transition to our new 'package tracker' on github. The new system will enable a more public review process where community …

news package submit package News

updated 9.6 years ago • Valerie Obenchain

http://www.probes.com/servlets/directory?id1=6&id2=48&id3=319 http://www.probes.com/media/publications/394.pdf As far as I know Limma accounts for dye bias during normalisation. If there is less/no bias will there

limma limma

updated 21.3 years ago • Matthew Hannah

Hi, We are using Illumina's VeraCode technology with the GoldenGate assay to investigate 192 SNPs in a case-control study. We are wondering if there is any software alternative to GenomeStudio to analyze the raw data. The beadarray package in Bioconductor seems like a possibility, but since Illumina's VeraCode and Illumina's BeadArray use somewhat different technologies, we are wondering if it …

microarray beadarray Illumina Veracode

updated 10.9 years ago • lacion

Is that the appropriate way to do this or is there a risk in revealing the manuscript before publication (as some journal requires some enclosure on the manuscript contents before it is published)? Thanks in advance

updated 13.3 years ago • Yue Li

t" "gene" "--extraAttributes" "gene_name" "-a" "/scratch/chunter/Merged/bonobo_chimp.gtf" "-o" "/public/home/chunter/Chonobo/alignments/Dennis/Merged/FullGenome/bonobochimp.fc" "/public/home/chunter/Chonobo/alignments...FullGenome/bonobochimp_aln.sam" Geneid Chr Start End Strand Length gene_name /public/home/chunter/Chonobo/alignments/Dennis/Merged/FullGenome/bonobochimp_…

DESEq2

updated 5.8 years ago • chunter

drug targets and predicting potential safety signals based on associations with traits in public datasets (e.g UK Biobank). * Using methods like Mendelian Randomization to identify causative genetic factors. * Exploring...to specialists and non-specialists and the academic research community through presentations and publications. * Contributing to Denali's overall human genetics strategy a…

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updated 7.6 years ago • sandmann.t

geneCountsUI[notZero, ], 1, function(y) { fit <- glm(y ~ groups, family = poisson(), offset = log(uq.scaled)) fit0 <- glm(y ~ 1, family = poisson(), offset = log(uq.scaled)) anova(fit0, fit, test = "Chisq")[2, 5] }) [[alternative HTML version deleted

updated 15.4 years ago • Johnny H

lt;- normalizePlates(x, normalizationMethod="NPI",negControls=negCtr, posControls=posCtr,transform=log) We get an error: Error in NPI(x, posControls, negControls) : 'posControls' should be a vector of regular expressions with length...normalizePlates(x,normalizationMethod="negatives",negControls=negCtr, posControls=posCtr,transform=log) this error doesn't occur. What is wrong in the definit…

Normalization cellHTS Normalization cellHTS

updated 17.7 years ago • Klaus-Peter Pleissner

the original counts (or the CPM? instead) are moderated to avoid infinite values when taking logs of samples/genes with zero counts/CPM, but I'm not quite sure that I can figure out exactly how this is produced. a) Is the same...by prior.count? c) Is there a way to see the moderated CPM for each gene and sample and not just the log (moderated CPM)? 2) How is the logFC calculated? Is it based on…

edgeR edgeR

updated 12.1 years ago • Guest User

for visualization purposes, I found the VST (setting blind=false) more effective than using the log-transformed normalized counts (with a pseudocount of +1) at stabilizing the variance over the mean. Rlog seems to just keep...scaled up, as would be expected, and biologically the results appear consistent between both the log-transformed normalized counts and the VST counts. Heatmaps of spec…

deseq2

updated 6.1 years ago • cafosspot

lt; 1e-10)) break : missing value where TRUE/FALSE needed In addition: Warning messages: 1: In log(1 - alpha * theta) : NaNs produced 2: In log(1 - alpha * theta) : NaNs produced sessionInfo() R version 2.7.0 (2008-04-22) i386-pc-mingw32 locale

CGH snapCGH CGH snapCGH

updated 17.3 years ago • Abhilash Venu

UNC Charlotte Dept. of Bioinformatics is seeking a full time Software Developer (research associate). The incumbent will lead the development of bioinformatics web servers, resources and applications. He/she will also work on big data integration and analysis. One focus is the Pathview project. Pathview is an open-source package that maps, integrates and renders a large variety of biological data…

php javascript rmysql R Job

updated 8.7 years ago • Luo Weijun

<div class="preformatted"> McGee, Monnie wrote: > Dear List, > > I have been searching the Internet for CEL files for the Golub (1999) AML and ALL CEL files. I am interested mostly in the training data (38 files - 27 ALL and 11 AML). Are they publically available? > The are not. > Second, if they are not, and all we have is the golubEsets package, …

Cancer Cancer

updated 19.2 years ago • rgentleman

advisor's comments on Barack Obama's admission of past drug use Friday, the New York senator's first public remarks on the matter since the advisor announced he was resigning from the campaign. At the same time, the film suggests...advisor's comments on Barack Obama's admission of past drug use Friday, the New York senator's first public remarks on the matter since the advisor announced he was r…

updated 18.1 years ago • MLeon DPagan

<div class="preformatted">Presenting the energy Co to be in for rest 2007 ENERBRITE TECHNOLOGI Symbol : ETGU Energy sector is hot right now, and everyone wants in About the Co We have two strategic objectives: ~ to become a market leader in developing and marketing innovative and intelligent energy saving solutions that achieve significant savings in the cost of energy and substantial im…

updated 18.1 years ago • Nigel Baca

to single-cell data preprocessing; Bioconductor-centric and Seurat-centric. The first typically uses log-normalised counts and the second typically uses `SCTransform` followed by centring and scaling, each followed by their

scran bluster scater scuttle

updated 21 months ago • Dario Strbenac

different read depths'. On the plot, on the y-axis, it says '**log10** BP'. I was wondering which log is actually used to generate the figure. Thank you very much in advance. Best, Etienne

ChIPQC

updated 4.5 years ago • etiennedanis

the biological duplicates. The simplest way I could think of is use the arithmetic means. For normal log transformation, that would means using the geometric means of the biological duplicates. But even for that I am not sure

deseq2

updated 8.7 years ago • JunLVI

Dear all, I am a edgeR user and I would like to know if edgeR reports 'average' cpm for each of the conditions tested in the analysis. Having a look at the output it seems the only information I have is the 'average' log(cpm) calculated using all the libraries. So the question would be, is there any way to output 'average' cpm (condition 1) and 'average...in the analysis. Having a look at the ou…

edgeR

updated 8.8 years ago • Anna Esteve Codina

div class="preformatted">Hi, I would like to know how to export non log transformed data from limma after normalization. Also, I would like to know if any of you have experience with among slide

Normalization limma Normalization limma

updated 21.9 years ago • Christian Landry

I  run the test and then I filter on logFoldchange and p-value ) and glmTreat (I choose the log fold change in the argument lfc of the function )  functions . Why such differences and which method is the good one ? Ty

edger

updated 7.8 years ago • Aurora

generating-pca-plots) describes, _by default, `` runPCA `` performs PCA on the log-counts using the 500 features with the most variable expression across all cells_. I am wondering how the most variable

scater pca features

updated 7.1 years ago • jws

Hello everyone, I am quite confused regarding the Log 2 fold change calculations. I noticed that it gives NA when the gene expression is zero across samples. But how does it calculate

deseq2 rnaseq

updated 8.2 years ago • AP

normexp' background correction method. The purpose of the offset is to reduce the variability of the log-ratios for low intensity spots, because the log-ratios M = log2( R / G) are damped towards 0 by larger offsets. The optimal choice...is the one which makes the variability of the log-ratios as constant as possible across the range of intensity levels. (This is the same general purpose as …

vsn limma vsn limma

updated 19.8 years ago • Gordon Smyth

in the reaction) which are to skip the `Seurat::NormalizeData()` step, but transform the data to log scale (which is stored in `object@metadata`) __prior__ to `ScaleData` and also note that log scale in Seurat is natural log. I

tximport Seurat Smart-Seq Smart-Seq2

updated 5.5 years ago • lshepard

of R's built-in install.package() and update.packages() is the creation of a separate installation log for every package. Further, if make is invoked with '-k', failure to install a single package will not derail the installation...wget -N -nd -r -A gz -r -l 1 -nv PACKAGE_FILES = $(wildcard *.gz ) PACKAGE_LOGS = $(addsuffix .log, $(basename $(basename $(PACKAGE_FILES)))) default: cran biocon…

updated 21.7 years ago • Kimpel, Mark W

Remove transcript version .** normMat <- txi.salmon$length normMat <- normMat/exp(rowMeans(log(normMat))) o <- log(calcNormFactors(cts/normMat)) + log(colSums(cts/normMat)) y <- DGEList(cts) y$offset <- t(t(log(normMat)) + o) <strong

salmon edger tximport rnaseq

updated 7.6 years ago • martin.weihrauch

div class="preformatted">I don't know of any packages designed for probe-level analysis, nor do I know what you mean by SFP detection. However, if you just want to use the probe values for analysis you can simply background

probe affy convert probe affy convert

updated 18.1 years ago • James W. MacDonald

of tumors only in A (TF), number of tumors only in B (FT), number of tumors found neither in A nor in B (FF). The data are in the form of 2x2 contingency tables. E.g. Gene 1 Gene 2 TT TF FT FF g1 g2 5 1 1 27 g1 g3 4 1 1 28 g2 g3 4 2 0 28 ... ... ... Notice

updated 13.5 years ago • Efthimios MOTAKIS

Hu6800 > > Dear BioC people > > Could it be that neither detection.p.value (simpleaffy) nor > mas5calls (affy) > work with Hu6800 chips? > > I get the following errors: > > > M17 <- ReadAffy(filenames=c("M17.cel

hu6800 probe simpleaffy hu6800 probe simpleaffy

updated 20.8 years ago • Claire Wilson

DESeq) to analyse base counts. The negative binomial assumptions of those packages would be grossly violated. However, the limma-voom pipeline for RNA-Seq data would remain valid for base counts, and is highly competitive with

limma edgeR DESeq limma edgeR DESeq

updated 13.9 years ago • Gordon Smyth

down-regulated, one of the underlying assumptions for DESeq2 (most genes do not change) might be violated, so any recommendations on how to deal with such cases would be VERY helpful.   <table border="1" cellpadding="1" cellspacing

deseq2 normalization sizefactors

updated 7.9 years ago • René

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

DOSE DOSE

updated 22.8 years ago • Lang Chen