Bioconductor Forum

Best way of presenting a sub-fraction of edgeR RNAseq > gene expression results in a publication > > > Hi! > We selected a priori 5 genes to analyse and want to include them in a > table for publication. > &gt

edgeR edgeR

updated 11.9 years ago • Gordon Smyth

and edgeR) model read counts as following a negative binomial distribution (NBD). According to the [Wikipedia page on the NBD](https://en.wikipedia.org/wiki/Negative_binomial_distribution), "...the negative binomial distribution

rnaseq

updated 9.5 years ago • kjo

y, method = "TMM") `` `` v <- voom(y, design, plot=TRUE) ``   `` lcpm <- cpm(y, log=TRUE) `` From EdgeR, it was recommended that lcpm could be used to generate heatmap with a prior.count. However, from https

limma

updated 7.2 years ago • Raymond

or `log2 + 1`) on the normalized counts before exporting to a csv? are there reasons that VST or log transformations might not be appropriate for exon counts? thank you

DEXSeq

updated 4.1 years ago • A

on the HG-U219 platform from Affymetrix. What I want to do is to compare our data to data from public databases such as GeneExpressionOmnibus or ArrayExpress, but unfortunately these data are all based on the HG-U133

Normalization convert ArrayExpress Normalization convert ArrayExpress

updated 14.8 years ago • Andreas Heider

using Limma. When I look at the MD plot after limma fit, I see a strong correlation between log-fold-change and average-log-expression. What could cause this odd behaviour and how can I fix it? Thanks, Gil <img alt="plotmd

limma proteomics

updated 8.2 years ago • gil.hornung

to Bioconductor. On Wednesday I followed the instructions and added my github username and public key here: <https://docs.google.com/forms/d/e/1FAIpQLSdlTbNjsQJDp0BA480vo4tNufs0ziNyNmexegNZgNieIovbAA/viewform

github package updates developers package development

updated 8.3 years ago • rtraborn

<div class="preformatted">Hi, I've been using the limma normalizeBetweenArrays function to perform cyclic loess normalisation on single channel microarray data (non-log transformed signal intensities). Amongst the normalised signal intensities returned is one negative value. There is nothing 'odd' about the corresponding original value in the input signal intensity file. I presume that …

Microarray limma Microarray limma

updated 12.0 years ago • MIKE STARKEY

mean is sensitive to outliers, would not make more sense that aveLogCPM() resembles rowMeans(cpm(y, log=TRUE, ...))) instead? In the old microarray days one would take the average of the log-fluorescent units to look at average expression

edgeR rnaseq limma independent filtering

updated 8.3 years ago • Robert Castelo

My question is: should I plot raw percentages, or percentages out of ipidr::normalize_pqn (..., log = FALSE) It is true that results are similar in both cases, but not identical. Thanks!! Regards, David

Normalization Lipidomics lipidr

updated 13 months ago • David R

Hi everyone, I am running DESeq2 on a public available dataset of RNASeq of mouse immune cells. I am getting the error: `75 rows did not converge in beta, labelled...Hi everyone, I am running DESeq2 on a public available dataset of RNASeq of mouse immune cells. I am getting the error: `75 rows did not converge in beta, labelled in...counts(object), locfunc = locfunc, : every gene…

DESeq2

updated 2.6 years ago • andrebolerbarros

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updated 13.8 years ago • Paul, Cristina

I am using is 4.2.1 4. I have checked many previous postings for example : http://yiqingxu.org/public/BigSurError.pdf those solutions did not work for me. Thank you for your help, Bogdan ps : The R Version : > R.Version() $platform...1] "" $major [1] "4" $minor [1] "2.1" $year [1] "2022" $mo…

limma Bioconductor edgeR

updated 3.2 years ago • Bogdan

is doing well :) I have a question regarding using LIMMA package for data that is not RNA-seq nor microarray. I have a dataset of protein/biomarker quantification(around 365 proteins) and I would like to get log-fold changes

Proteomics NPX limma

updated 4.8 years ago • r.i.s.alnuwaysir

the variance contributed by sampling distribution of LFC isn't separated out, unlike the prior for log dispersion. 2) The model's coefficients (LFC's) estimates for a gene should be correlated, while the priors for them are set

DESeq2

updated 7 months ago • Chenghao

The 'Home' shows:An error has occurred. Check your logs or contact the app author for clarification. I can't analyze the data

Reports

updated 20 months ago • 315005358

per million (CPM) and log2(CPM) as follow: > CPM <- cpm(x) > logCPM <- cpm(x, log=TRUE, prior.count = 1) The CPM matrix looks as expected but the logCPM returns negative values, and with a prior.count=1.0...values. Indeed if I compute log2(CPM+1), I get completely different values. So what is cpm(x, log=TRUE) returning? --- --------------------------…

edgeR cpm

updated 7.6 years ago • jxb.dev

I'm using DESeq2 to analyze differential gene expression between two groups. As I understand, the log fold changes for genes with low counts (low mean expression) should be shrunken toward zero, but in the MA-plot (see below...I'm using DESeq2 to analyze differential gene expression between two groups. As I understand, the log fold changes for genes with low counts (low mean expression) should be…

deseq2 rnaseq

updated 9.1 years ago • lostisle

with two groups Control(C1,C2,C3) and Treated(P1,P2,P3) having three replicates each. I need the log FC ratio with Treated(P1,P2,P3) value in the numerator and Control(C1,C2,C3) in the denominator but the results I am getting

edgeR edgeR

updated 14.2 years ago • Guest User

Hi Bioconductor users, has anyone published data using "limma" for microarray analysis and would point me to it? Thanks a lot, Julia

Microarray Microarray

updated 21.7 years ago • Julia Engelmann

this? I double checked my raw data and it rather looks as if the SAH group tends to have higher log fold changes in many gene compared to the control group (and not smaller logFC as in dim 1 of the graph). The plotMDS function...samples. ```r # Unsupervised clustering of samples library(wesanderson) lcpm <- cpm(dge, log=TRUE) par(mfrow=c(1,2)) col.group <- group col.group…

limma MultidimensionalScaling

updated 3.1 years ago • Katharina

of the normalized counts shows different mean and IQR. The expression data is not an affybatch nor eset object to apply rma nor DESeq respectively. Is quantile normalization the way to go

normalization cancer tcga

updated 10.7 years ago • ezz

my RNA-seq reads using bwa-mem and circular RNA quantification using sailfish-circ. I saw some publications using limma to analyze such datasets. However, I am getting strange results using LIMMA. Here is an example that...would welcome any suggestions for other tools designed for analysis of such dataset. Y axis label = log CPM X axis label = case / control Boxplot example is in the li…

limma R edger

updated 6.8 years ago • tan_pei_fang

indeed contain negative values. This makes sense considering that the count data had already been log transformed (and potentially normalized? I haven't been able to verify this in the cBioPortal documentation or in other...all values are >0. In discussion with other colleagues it has been suggested to simply 'undo' the log transformation prior to passing the count data to VST. How should …

variancestabilizingtransformation rnaseq cBioPortal deseq2

updated 7.6 years ago • Ben Morris

gene expression in a v2-dependent manner? We have arrived at the standardized Beta coefficient ([Wikipedia][1]) as an appropriate measure of effect size. My few questions are: Is it appropriate to compare standardized Beta

DESeq2 GLMs

updated 5.6 years ago • owen.chapman1

Hi,  Gviz is amazing to visualize genomic data (big thanks to the developers). I was wondering, it possible to plot the coverage in a log scale from an AlignmentTrack? I have been trying to do this by passing the parameter 'transformation' but I don't see any effect...data (big thanks to the developers). I was wondering, it possible to plot the coverage in a log scale from a…

Gviz gviz

updated 9.6 years ago • Alejandro Reyes

heatmap to display the differences in the simple and the complex heatmaps. Here you can find the log fold change values: ![enter image description here][1] And the corresponding z-scores: ```r lcpm.df.scaled <- t(apply(lcpm.df...none", margin=c(8,6), lhei=c(2,10), dendrogram="column") sessionInfo(R version 4.2.1 (2022-06-23)) ``` ![enter image description here][3…

heatmaps ComplexHeatmap

updated 3.1 years ago • Katharina

every row. Perplexing thing is that normalized counts are same for both the runs but pValues and log fold change values are still different. The only thing done differently from the earlier run is that I had to reinstall

DESeq2

updated 23 months ago • Kuldeep

DESeq2 but will be subsetting transcripts based on a pre-determined criterion. Does this sub-setting violate any assumptions make by the statistical package? In other words, does DESeq2 expect a minimum number of genes? Thanks

deseq2

updated 5.6 years ago • DataFanatic

and upon request provide letters of support and technical descriptions for research proposals and publications. • Actively collaborate with researchers both on and off campus on a wide range of projects and applications...Metabolomics facility users to ensure, at a minimum, that the facility and its staff are included in publication acknowledgements. Wherever possible and appropriate, contribute…

Metabolomics

updated 3.8 years ago • Jenny Drnevich

for a small (chloroplast) genome. I want to manipulate the scale layer but I don't understand nor can I find any documentation about what the "scale.unit" argument does nor what could be used. The help just says "Unit used

ggbio

updated 10.9 years ago • rwness

Dear all, I have two related questions: 1) Are the assumptions for normalization violated when comparing experimental conditions with different ploidy? 2) Does it make sense to perform differential expression

ploidy normalization rna-seq differential expression assumption

updated 8.8 years ago • aec

using limma+voom, leaving me with residuals *r1* and *r2*. Since *r2* and *r1* have already been log transformed, I believe I can take the logFC as r2-r1. Does this seem reasonable? Alternately, are there any other approaches

limma RNASeq voom

updated 20 months ago • taur.vil

statistic and therefore no need to rely on the prior assumed proportion. 2. The B-statistic is the log-posterior odds of differential expression. Naturally the posterior probability has to depend on the prior probability...gt;From: J.delasHeras at ed.ac.uk >Subject: [BioC] Limma: correct calculation of B statistics (log odds) >To: bioconductor at stat.math.ethz.ch > >…

Microarray Genetics limma limmaGUI Microarray Genetics limma limmaGUI

updated 19.7 years ago • Gordon Smyth

My supervisor has requested that I create coverage plots to visualize BAM alignments of RNA-Seq data. I though a good way to do this would be to use Gviz. We work on the model legume Medicago truncatula which does not have a BSgenome package so I though I'd try and make one. Following the vignette I...of RNA-Seq data. I though a good way to do this would be to use Gviz. We work on the model legu…

bsgenome biostrings Gviz

updated 10.3 years ago • gtho123

to do rlm normalization with respect to the IgG and anti-IgG levels as is depicted in quite a few publications.  The PAA package is very non-descriptive as to how to input the control data and how that control data will...only using the non-control proteins in the first elist to no avail.  Neither the vignette nor the package manual describes exactly how these files need to be s…

PAA protoarray IgG subscript out of bounds RLM normalization

updated 10.3 years ago • aaron.kelly

Noncentral Hypergeometric Distributions, however after my very shallow reading of the differences on [Wikipedia](https://en.wikipedia.org/wiki/Noncentral_hypergeometric_distributions), Fisher's Distribution makes conceptual

goseq

updated 3.7 years ago • Steve Pederson

many contributors. Type 'contributors()' for more information and 'citation()' on how to cite R in publications. Type 'demo()' for some demos, 'help()' for on-line help, or 'help.start()' for a HTML browser interface to help. Type 'q()' to quit...character(0) > library(ROC) > plot(hist(1:10,plot=F)) Error in xy.coords(x, y, xlabel, ylabel, log) : x and y lengths differ I w…

updated 21.7 years ago • witek

expressed genes. How to proceed with such a case? Should I trust the results if the assumptions are violated? Thanks, &nbsp

differential expression TMM normalization rnaseq edger

updated 8.7 years ago • aec

and macluster() for clustering (see code below). Now, I am wondering how to extract the log ratios (R/G) for each gene for each time point. The consensus() function plots these values, and I would like to know how to get

GO hgu133a maanova GO hgu133a maanova

updated 17.4 years ago • Heike Pospisil

fold change values for a cluster of genes when calculated with DESeq2. When I manually calculate the log fold change this doesnt happen, so I cant understand what is causing this. Using code on another help forum I have plotted...the log fold change values so you can see the cluster I am talking about (there are also a couple of genes in the positive axis). There...irlba_2.3.5.1 futur…

DESeq2

updated 2.8 years ago • Layla

with supervision and a track record of significant impact to the research field (high-impact publications and/or computational methods) - Considerable weight will be put on the research plan proposed by the candidate...profile as well as with the current research groups at the Centre (max 1-2 pages), CV and a list of publications (with 5 most significant publications indicated), a short researc…

Biology AI Machinelearning Precisionmedicine Norway

updated 3.8 years ago • nuru.saadi

expressed (around 10.000 DE of 20.000 genes). The assumptions of the TMM normalization are violated. How to proceed with such a case

limma TMM differential expression normalization rnaseq

updated 6.7 years ago • natalia_lt

in hypothesis testing might be calculated from gene >expression > data, a simple example being log fold change. Could such a measure >appropriately > be used in GeneSetTest (in the sense that it wouldn't violate any of

updated 14.9 years ago • r_1470

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GO Organism Apis mellifera goseq GO Organism Apis mellifera goseq

updated 13.9 years ago • Corby, Vanessa

groups against two different subsets of their control samples. The potential issue is summarized in [Wikipedia](https://en.wikipedia.org/wiki/Spurious_correlation_of_ratios). In short, the idea is that if there are gene expression

deseq2 correlation

updated 7.1 years ago • Cornwell, Adam

of bullying and intimidation. We have also changed the instructions to reporters of Code of Conduct violations to include screenshots or copies of the incidents whenever possible and without compromising their anonymity

biocon code-of-conduct Bioconductor

updated 4.9 years ago • Laurent Gatto

and the following error message : unhandled exception in Rgui.exe(MULTTEST.DLL):0xC0000005; Access violation Is this a known error ? and is there a fix? thanks [[alternative HTML version deleted]]</div

GUI multtest GUI multtest

updated 22.2 years ago • Josephine.Liang@uchsc.edu

Hello, I am currently trying out `geNetClassifier` to build a classifier for bulk RNA seq. However, I am somewhat unsure how exactly I should preprocess my counts before providing it to the `geNetClassifier` method. In the vignette it says: > Note that since the ranking is built though package EBarrays, the data in the expression set should be normalized intensity values (posit…

geNetClassifier Normalization

updated 3.8 years ago • nhaus

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ChIPpeakAnno ChIPpeakAnno

updated 11.4 years ago • Julie Zhu

I am currently running data analysis on QuantSeq data in Atlantic salmon. I initially worked with part of this data in 2022, and having sequenced more samples in the meantime, I reanalyzed everything. The issue I ran into while doing Over Representation Analysis is that I do not get the same results as in 2022. Now, in 2022, the reference genome assembly was [ICSASG_v2][1], while in 2024, the r…

Atlanticsalmon clusterPro Salmosalar AnnotationHub GeneOntology

updated 22 months ago • Filipe

div class="preformatted">Dear All, This is my 1st post to bioconductor so please bear with me if I violate any rule. I want to do pathway analysis on my Mycobactirum tuberclosis microarray data. I tried to explore and I got

updated 13.3 years ago • ashwani Kumar

Hi, We have some arrays where most of the genes are turned on under certain conditions. This violates the assumption that most normalization methods make. What would be the best way to handle such arrays? We are using

updated 16.7 years ago • He, Yiwen NIH/CIT

A member of the evaluation committee cannot play any role in regard to evaluating his/her own PhDs, nor also in regard to nominations where there has been a direct collaborative link (e.g. through joint publications). Nominations...to have been successfully completed in the 2008 calendar year. Awards are ratified by the CS Board. Publicity is made in the CS and other newsletters, and on relevan…

Classification Classification

updated 17.4 years ago • William Shannon

interception of > 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 in...and delete the email immediately. -- Hervé Pagès Program in Computational Biology Division of Public Health Sciences Fred Hutchinson Cancer Research Center 1…

Annotation GO Cancer BSgenome Biostrings BSgenome rtracklayer GenomicFeatures goseq GO

updated 13.9 years ago • Hervé Pagès

Salmon 2. Import data to DESeq2 with tximport 3. Identify differential expression with a (varying) log-fold change using apeglm, resulting in S-values and a significance threshold of 0.005 was applied. We have repeated this

deseq2

updated 6.7 years ago • Jack.Hearn

<div class="preformatted">I'm working with a group that had an outside vendor run four Aglient 2-color oligo arrays for two control samples labeled with Cy3 (C1, C2) and four mutants labeled with Cy5 (M1, M2, M3, M4). Array 1: C1 vs M1 Array 2: C1 vs M2 Array 3: C2 vs M3 Array 4: C2 vs M4 The outside vendor sent them four spreadsheets, one for each array, containing normalized Cy5/Cy3 log…

Annotation GO annotate oligo Annotation GO annotate oligo

updated 14.1 years ago • Stephen Turner

Hello, I am pretty new at this and trying to colour my volcano plot based on up and down regulated genes, but when I run it it says: Error in `check_aesthetics()`: ! Aesthetics must be either length 1 or the same as the data (499): colour This is my code: ``` keyvals <- ifelse(p$log2FoldChange < -0.5 & p$padj > 0.05, 'darkorange', ifelse(p$log2FoldChange > 0…

EnhancedVolcano

updated 3.2 years ago • patrirodry85

The format of the data containing only integers suggests that the input should not be normalised or log-transformed in any kind of way. Also, the vignette describes no prior normalization of these data. On the other hand, several...publications I have read mention that they use normalized count data for GSVA. What is the appropriate type of input for using

rnaseq rna-seq preprocessing gsva

updated 9.4 years ago • t.kuilman

is a list of 524 molecular subtype labels at this link:__ https://tcga-data.nci.nih.gov/docs/publications/brca\_2012/  It's found as an answer to a __Biostars question here:__ http://tcga-data.nci.nih.gov/docs/publications...of human breast tumors"; _Nature_ 2012) __found here:__ https://tcga-data.nci.nih.gov/docs/publications/brca\_2012/   __Here's a guide…

tcgabiolinks tcga-brca gdc pam50 rna-seq

updated 7.8 years ago • pfrancislyon