Bioconductor Forum

Dear Prof. Love, I was wondering if you could help me with a query about the DESeq2 package in R please. I have sequenced RNA transcripts from six separate species and am comparing gene expression between pairs of species. The issue I am facing is that I cannot work out how to account for gene length when normalising the read count data, but I understand this is essential to do so when comp…

Normalization DESeq2

updated 2.3 years ago • cm15245

variation and that it also assumes most genes aren't differentially expressed. As my data violates 2/3 of these and perhaps the final one too (I don't know), I'm guessing this is a problem. However, I'd be very grateful if someone

DESeq2

updated 2.9 years ago • GLFrey

normal distributions. I've seen references to monte-carlo simulation studies to look at assumption violations but being at a biological institute it's difficult to get access to good statistics texts. All internet searches

updated 20.8 years ago • Matthew Hannah

ribosome bound RNA. We thought that in this situation the assumptions of DESeq2 normalization are violated. Therefore we thought to add ERCC spikes to the samples for the normalization. We thought of the following workflow

deseq2 translation efficiency spikes ribosome profiling

updated 9.2 years ago • GFM

wrote: 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

Normalization vsn limma Normalization vsn limma

updated 16.7 years ago • Alicia Oshlack

div class="preformatted">Hi everyone, I was wnodering the defualt (0.003,0.007) is for log-transformed or non-log trasnformed data. Thakn you in advance </div

updated 14.1 years ago • Ali Mohammadian

to other tiling arrays regardless enrichment strategy. We agree with that. The paper defined log ratio mi = qi + ei where qi = -log(1-pi). pi represents proportion of methylated CpGs at a given locus i, ei is an error term. By this definition...larger qi represents more methylation in methyl-depleted arrays. However, for MeDIP, qi should be log(pi) instead of -log(1-pi). We are wondering if anyo…

Normalization Normalization

updated 13.9 years ago • Johnny

in other samples but not in that sample. 2) question regarding counts and control samples: Are log transformed read counts used for the  differential binding analysis? If log transformed counts are used then how...does Diffbind normalize ChIP read counts with respect to control read counts- does it subtract log transformed control read counts from log transformed chip read counts or doe…

diffbind

updated 9.9 years ago • chintan_80

packages/release/bioc/html/rDGIdb.html sessionInfo() R version 4.2.0 (2022-04-22) Platform: x86_64-apple-darwin17.0 (64-bit) Running under: macOS Monterey 12.4 package.version("rDGIdb") [1] "1.22.0

rDGIdb

updated 3.6 years ago • Jannah

on human sequences, the p-value column in the report from groupReport() is actually "_an average of log(P-values) of individual sequences_" (from the vignette). I have a few questions: 1. Why not recompute the p-value after averaging...the log(p-values)? The column is still labelled p.value, which is misleading. Also, -log10(p-value) is more commonly used than log(p-value

pwmenrich log

updated 10.4 years ago • enricoferrero

I was following the OSCA book with one sample from my data that is from a pdx model, and when I arrived to the feature selection chapter and checked the mean/variance figure I got this: ![mean/variance log expression][1] It is very strange for me that mean of log-expression seems to be in the tens of thousands. The code that I have use: ```{r} sc_test <- read10xCounts(here("fil…

single-cell SingleCell SingleCellExperiment SingleCellWorkflow SingleCellData

updated 7 months ago • Konstantinos Yeles

<div class="preformatted">Using both mouse and human Sentrix-6 beadarrays, I've managed to normalize the arrays both with the beadarray package and the BeadExplorer package. However, despite being able to get an exprSet from beadarray and a BeadSummaryList from BeadExplorer, I'm not sure how to go to Limma from there. The exprSet does contain normalized values for all of the arrays, and I…

GO limma beadarray BeadExplorer GO limma beadarray BeadExplorer

updated 19.4 years ago • Anand Patel

to the sce object as gene names. I could not find an option in read10xCounts to eliminate these rows (nor were google searches productive). Why are CMO tags added as genes? Is this a bug or expected? ``` > h5file h2 "sample_filtered_feature_bc_matrix.h5

DropletUtils droplet

updated 2.1 years ago • pcantalupo

probes are within a specific genomic region (chromosome, start, stop). I am not sure if Biomart nor the annotation.db can do this as they both go to some common ID first. The annotation.db stuff seems to only have one position

Annotation GO Cancer biomaRt Annotation GO Cancer biomaRt

updated 17.6 years ago • Daniel Brewer

I am unable to create a biom (JSON, aka BIOM 1.0.0) format file using the biomformat package. Here is my attempt to make a simple biom (JSON) file: <pre> library(biomformat) otu <- as.data.frame( matrix(rpois(9,10),nrow=3) ) rownames(otu) <- c('OTU1','OTU2','OTU3') colnames(otu) <- c('Sample1','Sample2','Sample3') write_biom(make_biom(data=otu),'test.biom')&…

biomformat json

updated 8.9 years ago • grp2009

My point is that I have just 1 sample TREATMENT and 1 sample REFERENCE. Neither technical replicates nor biological replicates are available. A statistical test to find differentially expressed genes between the two conditions

Microarray Microarray

updated 13.4 years ago • Eleonora Lusito

it fails: Error: 'getBroadSets' failed to create gene sets: msigdb_v2.1.xml does not seem to be XML, nor to identify a file name Thanks a lot! Paul -- Paul C. Schr?der PhD-Student Division of Proteomics, Genomics & Bioinformatics

Proteomics GSEABase Proteomics GSEABase

updated 17.9 years ago • Paul ChristophSchröder

make it work without a orgPackage option (though in the examples from the vignettes it is not used nor mentioned). edit: I finally was able to make goProfiles work with the basicProfile() parameter idType = "GOTermsFrame". This

gosemsim go gene ontology

updated 10.7 years ago • cpcantalapiedra

<div class="preformatted">Hi All First of all, thanks for helping with normalize.quantiles function. I am trying to normalize intensity data from 4 different CEL files using normalize.quantiles function. However I understand that this function needs a matrix of data. I need to somehow try to map the intensity data from 4 CEL files to the same probe position and put it in a new file before…

Normalization cdf probe affy BufferedMatrix Normalization cdf probe affy BufferedMatrix

updated 16.6 years ago • Radhika Ambatipudi

if (missing(geoMeans)) {<br/>         loggeomeans <- rowMeans(log(counts))<br/>     }<br/> ...</code> <code>   sf <- if (missing(controlGenes)) {<br/>         apply...cnts) …

deseq2 sizeFactors

updated 8.2 years ago • katzman

Hi, I am using GenomeGraphs to generate gene structures. My codes are below: A few questions that I have 1) How to include the cytoband information e.g. 4q to the ideogram ? How to label the gene in the cytoband with "IL8" ? 2) What colour is actually used by gene and transcript ? I have created a legend with "orange" and "lightblue", but the colour doesn't look the same. 3) How to make the le…

affy biomaRt ideogram GenomeGraphs affy biomaRt ideogram GenomeGraphs

updated 17.1 years ago • Daren Tan

I keep running into the same error when trying to do a genes-to- pathways request in the KEGGsoap package: I'm new to the package, but as I understand it I should be able to pass a vector of gene IDs and receive back a vector of pathway IDs, however I keep getting a 'xmlns: URI SOAP/KEGG is not absolute' error. This appears to be something to do with the URL for the SOAP server: >> genes …

KEGGSOAP KEGGSOAP

updated 14.0 years ago • seth redmond

gt; ensembl=useMart("ENSEMBL_MART_ENSEMBL", host="www.ensembl.org") Space required after the Public Identifier SystemLiteral " or ' expected SYSTEM or PUBLIC, the URI is missing Error: 1: Space required after the Public...Identifier 2: SystemLiteral " or ' expected 3: SYSTEM or PUBLIC, the URI is missing Does anyone know how to fix this problem? Thanks a lot, Stefanie </div

biomaRt biomaRt

updated 14.9 years ago • Stefanie Carola Gerstberger

in tmp[1, ] : incorrect number of dimensions In addition: Warning messages: 1: NaNs produced in: log(x) 2: NaNs produced in: log(x) 3: NaNs produced in: log(x) 4: NaNs produced in: log(x) [[alternative HTML version deleted]]</div

gcrma gcrma

updated 22.4 years ago • Phguardiol@aol.com

expression changes than control group from before the diet to after the diet. So here, instead of log normalized intensity data, I am using log2 ratio of end of study intensity and baseline intensity as the dependent variable...I was wondering can this be modeled using limma? To my best understanding, limma expects log normalized gene expression and not ratio of log normalized gene expression at…

Microarray DifferentialExpression

updated 3.6 years ago • S

use? A logistic regression suggests that both factors are important: model <- glm(sig~ log(expression+0.1) * log(length) , data=retained_genes, family=binomial("logit")) retained_genes$preds = predict(model, type="response...Resid. Dev Pr(>Chi) NULL 6676 4507.1 log(expression + 0.1) …

goseq dexseq

updated 8.4 years ago • i.sudbery

two things > are verbo-algebraically the same (yup, new word. My next move is to > start a new Wikipedia entry describing exactly what it means ;-D) > > > > > My code is below. > > > > > > Thank you, > > Lev. > > > &gt

updated 17.8 years ago • Sanjat Kanjilal

below 1 leads to warnings that this will cause negative values during processing. But my data is not log transform, so I don't want to run using the "noLogTransform=TRUE" option assigned - I want NormalyzerDE to log-transform my

normalyzerde

updated 6.1 years ago • Jakob Willforss

class="preformatted">Dear Bioconductors, I am wondering whether it makes sense to use genes with log odds less than 0 generated from Limma. There are only a handful of genes with B>0. I observe the volcano plot of log odds vs...log ratios, and it seems to me that even with B = -2, there is a pretty distinct group of genes that can be separated from majority

limma limma

updated 20.8 years ago • Wu, Xiwei

Hello, I recently used WGCNA to analyze a 15 sample set (7 cases and 8 controls), and it appears to have worked swimmingly. The analysis yielded a resulting module highly correlated to disease status (.7) and the GO results are highly consistent with previous literature for this disease. Looking forward to in vitro validation experiments! Looking back on the theory of WGCNA, I am unclear as to …

WGCNA Theory Scale-Free Topology

updated 10.8 years ago • brohawndg

HTTP traffic: Item: http://cran.r-project.org/src/contrib/XML_1.95-3.tar.gz Action: deleted Reason: Violation of a compressed file restriction -- File: XML_1.95-3.tar.gz, security warning: Corrupted_Zip_file The uncleanable

updated 17.5 years ago • raffaele calogero

30 (B) = 1210. Both `rep1_A` and `rep1_B` would therefore be normalized by this value. Would this violate the assumptions of normalization (e.g. TMM) or the DEG tests? Thanks! The dataset is essentially analogous to this (however

deseq2 edgeR normalization DGE

updated 6.2 years ago • grant.dejong

<div class="preformatted"> Hi: Over the past couple of years my laboratory has become interested in scholarly communication. To this end we have established a resource www.scivee.tv <http: www.scivee.tv=""></http:> where you can upload scientific video content. Of particular interest, and the reason for this email, is the ability to upload a 5-10 minute video describing your …

updated 18.3 years ago • Phil Bourne

So I have a biological question that seems best understood as a change in ratio of two sequenced products between two conditions. So given a design of `counts ~ condition` the null hypothesis is that for each gene `A` and a fixed reference `B`: `log(mu_A_condition1) - log(mu_B_condition1) >= log(mu_A_condition2) - log(mu_B_condition2)`. This is partially derived from the need to treat the …

DESeq2

updated 4.5 years ago • Martin Modrák

from original command, because on my understanding, there were no rows to be skipped, nor comments.) error colSums(x$counts) : 'x' must be numeric This error message might be inaccurate, because it is localized. GAT.txt

GUI edgeR GUI edgeR

updated 15.2 years ago • 村田卓也

for a large number of paired-end gzFASTQ files using the align() function, and have been careful to log all of the output to keep track of summary information and any error/warning messages that may have been produced. Of the...as they have a PCGC account. Here are the remote paths: <pre> resrhdxp01.research.chop.edu:/pcgc/public/Other/transcriptome/fastq/PCGC0065312_HS_TX__1-02059__v1_FC…

rsubread bug alignment

updated 11.2 years ago • caufeminecraft

group), ylab="PAXB",xlab="group") Error: Error in plot.window(xlim = xlim, ylim = ylim, log = log, yaxs = pars$yaxs): need finite 'ylim' values

boxplot bioconductor R error

updated 6.1 years ago • l154359

data from our collaborators. For individual sample, there are 7 corresponding columns: Unknown:Log(Ratio) Unknown:Ratio Unknown:Fold Change Unknown:Log(Error) Unknown:P-Value Unknown:Intensity 1 Unknown:Intensity 2 It...seems that Ratio= Intensity1/Intensity2. I wonder whether I should use log2(Ratio) or Log(Ratio) or just Ratio for further analysis. Besides, why should Ratio be calculated…

updated 17.6 years ago • affy snp

Hi, I (sadly) only have one RNA-seq sample for each condition and want to use log fold change to determine whether the feature counts is different in one condition relative to the other. Apparently...Hi, I (sadly) only have one RNA-seq sample for each condition and want to use log fold change to determine whether the feature counts is different in one condition relative to the other. Apparently, …

deseq2

updated 9.7 years ago • Chao-Jen Wong

Dear Julien, The component 'Amean' in the output from lmFit() is supposed to hold the mean log-intensity for each probe, an indicator of the overall expression level of the corresponding transcript. However, if the...data values input to lmFit() are log-ratios rather than log-intensities, then there is no way to compute the mean log-intensities. If the first argument to lmFit...in your simulati…

probe limma probe limma

updated 18.9 years ago • Gordon Smyth

host="ubio.bioinfo.cnio.es", port="9002", path="/biomart/ martview/") Space required after the Public Identifier SystemLiteral " or ' expected SYSTEM or PUBLIC, the URI is missing Error: 1: Space required after the Public...Identifier 2: SystemLiteral " or ' expected 3: SYSTEM or PUBLIC, the URI is missing Latest version of biomaRt does not support 'mysql' anymore (which worked!) and we can't ma…

Cancer biomaRt Cancer biomaRt

updated 16.4 years ago • Daniel Rico

div class="preformatted"> Dear list, Are the Log2 ratios in our MAlist the log ratios of test sample/reference sample? or the log ratios of Cy5/Cy3 as when we run normalizeWithinArrays in Limma? I am confused

updated 18.3 years ago • caiwei@mdanderson.org

just can't handle the chip type right now. So can somebody work on that to make it available for public or if not for public right now, can somebody make an R package for me to install the cdf packages of 100K and 500K cdf files

SNP cdf SNP cdf

updated 20.2 years ago • Zhang, Jacob Zhongfa

GSVA was performed based on RNA-Seq Row Count data, which was normalized by edgeR::cpm(count, log = T). However, the enrichment score show many negative value, which was not observed when parameter method is 'ssgsea'. (1) Is it...value? Any suggestions would be appreciated! ```r gsva(expr = as.matrix(edgeR::cpm(count, log = T)), gset.idx.list = hallmark, method = 'gsva', …

GSVA RNASeq edgeR

updated 3.5 years ago • Yang Shi

the limma pipeline. Is there a convenient way to transform my normalized expression dataset into log expression values and an object that is compatible with lmFit command? If not, do you have suggestions which package might...weights=NULL, # method="ls", ...) #object #A matrix-like data object containing log-ratios or log-expression values for a series of arrays, with rows #corresp…

limma MicroarrayData

updated 3.5 years ago • waltheja

metric for within-sample correlation between genes (I'm doing pairwise for genes).** - TPM or log(TPM); - CPM or log(CPM); - CPM + TMM (edgeR); - log(counts) normalized by median of ratios method (DESEq2); So far I'm inclined towards simply

edgeR Normalization DESeq2 tpm RNASeq

updated 5.2 years ago • tcalvo

maxit) should be performed until there is no convergence. 1) Would it make a difference if I log and do the cyclic loess or use unlogged dataset to perform cyclic loess(by mentioning in the function log.it=F)? I am asking...this because in the microarray dataset of 48 samples when I log then it goes on and on and never gives "no convergence" for atleast 10 iterations that I tested.But when I use …

Microarray Microarray

updated 15.0 years ago • viritha kaza

Hello, I just need someone to clarify whether the logFC column in the toptags dataframe is log base 2 or log base 10. I was unable to see this information in the manuals. Thank you very much. best wishes, Chris [[alternative

updated 13.0 years ago • Christopher T Gregg

Hi, I am using edgeR to analyze differential expression of my RNA-Seq data. I am getting a plot of log-fold change vs log-counts per million with plotSmear function. I am wondering how can I export all the data as excel file

edger

updated 9.3 years ago • linya

conditions, but that there is a lot of variability between the replicates. This is exactly what the log-ratio analysis would tell you. On the other hand, if you average the fold changes, you get nonsense results. The two fold changes...expressed the fold changes the other way around. It is necessary to express the fold changes on a log-ratio scale, so that multiplicative changes become additive…

limma limma

updated 20.7 years ago • Gordon Smyth

too but it only has LogNormalization. I believe it just takes the logarithm (in Seurat it is natural log not log2 I think). I want to use deconvolution method which is provided by Scater package. Convert() function of Seurat transforms...and converted it to SingleCellExperiment object, normalised it (without transforming values to log). What should I do now? I can convert the SingleCellExperimen…

scater seurat singlecellexperiment rnaseq

updated 7.1 years ago • hamza_karakurt

aveage spots. Each spot was printed twice in my cDNA array, how limma average them? I have all the log ratio from every printed spot(twice printed). When I did correlation between replicated, their coef is very low, which compared...to arrayTool analysis, is significant different. When I looked at the log ratio, limma has twice as many as arrayTool log ratio, so I think limma did not average my s…

limma limma

updated 21.8 years ago • Joyce Gu

useMart("ENSEMBL_MART_ENSEMBL", host="www.ensembl.org") I get : >Space required after the Public Identifier >SystemLiteral " or ' expected >SYSTEM or PUBLIC, the URI is missing >Error: 1: Space required after the...Public Identifier >2: SystemLiteral " or ' expected >3: SYSTEM or PUBLIC, the URI is missing Does anyone know how to fix this problem

GO biomaRt GO biomaRt

updated 14.9 years ago • Stefanie Carola Gerstberger

not differentially expressed, for the default workflows to work well, and the impact of assumption violations

edgeR DESeq2 Transcriptional Amplification

updated 6.8 years ago • Dario Strbenac

estimateSizeFactorsForMatrix lines 44-46 ```r if (incomingGeoMeans) { sf <- sf/exp(mean(log(sf))) } ``` what ends up happening here is that the calculation sf/exp(mean(log(sf))) is saying that every number is NA. However within...sf value within the sf vector. Thus ```r if (incomingGeoMeans) { sf <- sf/exp(mean(log(sf))) } ``` produces values that are all …

DESeq2

updated 4.5 years ago • alawrence2211

for the great effort of bringing this forward, I was waiting for this since the *Neither random nor censored* Bionformatics manuscript. Reading `limpa`, it is not clear to me if one should still gain for TREND=TRUE in `eBayes

limpa limma trend

updated 8 months ago • Alejandro

target, object, assay, slot, adjustment) : celltype is not a metadata or gene nor equal in length to ncol('object') sessionInfo

imcRtools SingleCellData imcdatasets SpatialWorkflow

updated 24 months ago • Simon

symbols) the normalized intensity distribution appears to be very biased (boxplots are not centered nor have even distributions anymore). I think this could be explained by differences in RNA biotype composition (real or perhaps

oligo

updated 4.4 years ago • Lauro Sumoy

Hello, I'm analysing RNA-seq data from two datasets (from healthy samples) and created a unique GTF file to identify new isoforms by using StringTie. Then I used Salmon to estimate their TPMs, but I have some questions hoping anyone can help me: 1) Besides PCR, how do I know that these putative novel transcripts are not "transcriptional noise"? 2) I used *tximport* to import my Salmon ou…

tpm RNASeq tximport

updated 4.4 years ago • karlaarz

charset="us-ascii"; format=flowed Dear Mark, If I understand your problem correctly, neither GSEA nor GSA will accomodate it. The only option I know of is geneSetTest() in the limma package. This generally works well, although

updated 18.9 years ago • Simon Lin