Bioconductor Forum

https://repo.miserver.it.umich.edu/cran Bioconductor version 3.15 (BiocManager 1.30.17), R 4.2.0 (2022-04-22 ucrt) Installing package(s) 'TxDb.Hsapiens.UCSC.hg38.knownGene' installing the source package ‘TxDb.Hsapiens.UCSC.hg38.knownGene

Install

updated 3.7 years ago • BioC123

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software error ggplot2

updated 5.5 years ago • yueli7

The following biomaRt query returns the minor\_allele column as logical instead of character:   <pre> library("biomaRt") mart <- useMart(host="feb2014.archive.ensembl.org", biomart="ENSEMBL_MART_SNP") ensembl <- useDataset("hsapiens_snp", mart=mart) res <- getBM(attributes=c("chr_name","chrom_start","chrom_strand","allele","refsnp_id", "refsnp_sou…

biomart getBM logical error

updated 10.0 years ago • Christian Ruckert

Hello! What is the true definition of MA plot? The limma::plotMA displays Expression log-ratio of one sample vs. others even with NGS platform data. My understanding is this package was developed for microarrays...were useful to see one sample/array vs. others. I could not find an explanation for how to look at log-ratio for the mean expression of all NGS platform data in an experiment in the li…

limma plotMA

updated 10.4 years ago • Lisa Cohen

log2 transformed values because the negative binomial GLM already handles heteroscedasticity and the log link function ensures the model coefficients are log2 fold changes. `limma`'s choice to use a regular linear regression...to meet homooscedasticity it needs to reduce the heteroscedasticity of the intensity data with a log transform. If this is true, why doesn't `limma` avoid requiring log2 tr…

limma DifferentialExpression DESeq2

updated 4.6 years ago • tjbencomo

So I wonder: how are the mm- values estimated? I cannot find information on this in the NEWS file nor somewhere else. And is there some information available on the reliability of the calculated MAS5-values and corresponding

affy affy

updated 15.7 years ago • Groot, Philip de

Hi. When running the DEseq command, it proceeds to the "fitting model and testing" step where stalls longer than it should and then exits with this. <pre> > dds < DESeq(dds) estimating size factors estimating dispersions gene-wise dispersion estimates mean-dispersion relationship final dispersion estimates fitting model and testing -- replacing outliers and refitting…

deseq2 R

updated 8.7 years ago • Jacob Stauber

normalization be the "best" way to start [as suggested here][1]? Or, sum normalization followed by log and then z-scaling [as here][2]? Or, perhaps even TMM normalization as [one possibility implied here][3]. I have also had median...by log normalization suggested to me. I think all agree on taking log, but I wonder if we need to start with sum or median normalization...and then what if anything …

Lipidomics Metabolomics limma Normalization

updated 4.5 years ago • pgugger

it can't find file `aux_info/meta_info.json`. Indeed, there are no such file, neither in the cache, nor in the indices, nor with the `quant.sf` files. I am not sure what I am doing wrong here. I am using salmon 0.14.1, and the sessionInfo

deseq2

updated 6.2 years ago • eric.blanc

RUV normalization, what do you use as an input for the RUVphospho() function? Do you use a matrix of log-transformed raw peptide intensities or do you first normalize the log-transformed intensities using Z-normalization

PhosR

updated 3.6 years ago • Ismail

packages/release/bioc/vignettes/Heatplus/inst/doc/annHeatmap.pdf) does the legend represent log fold change? In figure 3 (the correlation heatmap), does the legend relate to log fold change or correlation values? Thanks

Heatplus Heatplus

updated 13.1 years ago • Hoyles, Lesley

do within arrays normalization just subtract over the whole array ( or witnin i-th block) mean of log- ratio of spike control from log-ratio for each gene). I use Limma. My question is: does limma have options for such normalization

limma limma

updated 20.5 years ago • NATALIA F TCHETCHERINA

with: eset=rma(Data); Set=vsn(eset); I know that medianpolish does log2 transformation and vsn does log transformation (base e), but when I compare the results, the difference between the two datasets is huge- not a matter of log

vsn vsn

updated 21.9 years ago • Julia Engelmann

Hi, I just wanted to get some clarification on MA plots and exactly what they represent. Including one I made of my diff peak data. I am wondering what the darker blue area is close to the origin as well as further down the log concentration and exactly what it represents in comparison with the lighter blue? Also maybe in this context what is the...data. I am wondering what the darker blue area …

diffbind ma plot

updated 8.9 years ago • rbronste

this option the input object should contain raw intensities, i.e., prior to background correction, log-transformation or any normalization. Note that the normalized intensities are on the log-2 scale, not the log-e scale output...this statement from ?normalizeBetweenArrays ("Note that the normalized intensities are on the log-2 scale, not the log-e scale output by the vsn function in the vsn pack…

Normalization vsn limma Normalization vsn limma

updated 16.4 years ago • Guido Hooiveld

developer group" was formed 2 days ago, we (I) only later realized that we should have created a public list for the same project simultaneously which I now have done. Bioconductor := Public Mailing List for Discussion about...for a few weeks! Both Robert and I have full ``List Admin'' priviledges. Note however that for the public "Bioconductor" List, users can do everything themselves (by t…

updated 24.1 years ago • Martin Maechler

to a value of 10 for the same gene in a different experiment? One other question I had was on a log odds plot is the log fold change a log based 10 measures so that a change of log fold change 1 would be 10 in reality? Is this

updated 21.4 years ago • Elizabeth Brooke-Powell

creating logcounts (I assume this is the CPM of the log2 count) logcounts <- cpm(dgeObj,log=TRUE) Third, I tried to get the TMM normalized count, and here is my question. I used this code dgeObj <- calcNormFactors(dgeObj...logCPM <- cpm(dgeObj, log = TRUE) I first make TMM normalization on the dgeObj, then used cpm function with log =TRUE on this dgeObj …

RNASeq R edgeR

updated 3.5 years ago • Mohamed

a change to the code for MAplot. When you call MAplot(pairs=TRUE) for Affybatch objects, double logs are taken; you can see this in the affy vignette (Oct 13, 2005) on pg 11 - the A values only range from 2 - 4. MAplot by default takes...the logs, but so does mva.pairs, which is called when pairs=T. One solution is to use MAplot(abatch, pairs=T, log=F) , but it would easier

affy affy

updated 20.1 years ago • Jenny Drnevich

to me " a LOWESS curve is fitted to square-root standard deviations 𝑠1/2𝑔 as a function of mean log-counts 𝑅" but it seems to me we'd really like to fit the LOWESS curve as a function of r which is the mean gene level count and...mean of the library size. I think this is the case as we'd like to model variance by the mean log count of each gene and then use that to model the variance of each obs…

voom

updated 7.1 years ago • njbernstein

at the documentation and it would indicate in the transform argument that the default is to use log. When I look in the documentation for log() I see that the default is e. I thought this didn't seem right so I ran a quick test comparing

scuttle scater

updated 2.4 years ago • Abbi Edwards

TCGA. The size is 577 samples with number of genes 18.522. When I tried to run DESeq2 to calculate log foldchange, it took not that long, around 3-4 hours. After that, I want to use rlog function to get the log transform of gene expression

deseq2

updated 10.0 years ago • bharata1803

The data has been quantified and normalized using the LFQ method - the sample distributions are log normal, but with a high median 10e7, ranging from 0 to 1e10 The problem arises with genes that are present in one condition...and absent another. Before putting the values into limma I need to log them, which converts 0 - Inf, and drops the genes from the analysis. I tried replacing Inf with 0 or …

limmagui proteomics

updated 10.1 years ago • vedran.franke

is after normalization of two color microarray data, whether arrayQualityMetrics should be run on M (log ratios) matrix or A (average log intensity) matrix ? I am guessing it should be run on A matrix as arrayQualityMetrics requires

Microarray Normalization arrayQualityMetrics Microarray Normalization arrayQualityMetrics

updated 15.7 years ago • Amit Kumar

T, s0=NA, include.zero=F, delta=seq(0.1,5,0.05) ) ## plot to observe the values (the version with -log() to see the difference in the small pvalues) #plot(sam.out at d[order(sam.out at d)],samr.obj$tt[order(samr.obj$tt)]) #plot(-log(sam.out...at d[order(sam.out at d)]),-log(samr.obj$tt[order(samr.obj$tt)])) plot(sam.out at p.value[order(sam.out at p.value)],pv.samr[order(pv.samr)]) plot(-log(sam…

siggenes siggenes

updated 17.7 years ago • Cécile Laurent

lt;- calcNormFactors(x1, method = "TMMwzp") # unormalized lcpm <- cpm(x1,log=TRUE,prior.count=5) boxplot(lcpm, las=2, col=col, main="") title(main="A. Unnormalized data",ylab="Log-cpm") #normalized #TMM lcpm_TMM...lt;- cpm(x1_TMM,normalized.lib.sizes = TRUE, log=TRUE, prior.count=5) boxplot(lcpm_TMM, las=2, col=col, main="") title(ma…

edger limma voom normalization limma

updated 7.1 years ago • Konstantinos Yeles

parseKGML2Graph(cancerKGML,expandGenes=TRUE); I get: Error: XML content does not seem to be XML, nor to identify a file name '' Any ideas? Many thanks, Eric -- output of sessionInfo(): R version 2.15.0 (2012-03-30) Platform: x86_64-unknown

KEGGgraph KEGGgraph

updated 12.9 years ago • Guest User

<div class="preformatted">I'm sorry to trouble you guys. I have a doubt about my design matrix. I have RNA-seq data for 2 different genotype of trees with 0hour(control) and after treatment 3hours,24hours,and 48hours. The experiment design like following: Treatment Tree H1 Ctrl 3hrs 24hrs 48hrs Tree H2 Ctrl 3hrs 24hrs 48hrs Tree L1 Ctrl 3hrs 24hr…

ASSIGN ASSIGN

updated 13.6 years ago • KJ Lim

to create the annotation package for GPL10427. It is ovine species platform, and there is no .db0 nor schema for it. I'm trying to read 'Creating an annotation package with a new database schema'. It's ashamed of me, but I'm an R beginner

Annotation db0 Annotation db0

updated 12.3 years ago • Guest User

zebrafish.db0 * mouse.db0 * bovine.db0 * human.db0 In addition, it is not clear to me (nor can Marc recall) where the data for PFAM in the yeast.db0 package comes from. Given that we are pretty far behind schedule

annotation proteomics uniprot.ws News

updated 10.3 years ago • James W. MacDonald

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 • Warnes, Gregory R

272352 #> # Db created by: GenomicFeatures package from Bioconductor #> # Creation time: 2022-09-27 15:30:34 +0000 (Tue, 27 Sep 2022) #> # GenomicFeatures version at creation time: 1.49.6 #> # RSQLite version at creation time

microRNA TxDb.Hsapiens.UCSC.hg38.knownGene

updated 3.0 years ago • Lluís Revilla Sancho

Hi. I am very new to bioinformatics/programming. Running the code for the first time *ever* using atena package (following their manual). I got the following error. What am I doing wrong? I have attached my full working screen's screen shot for reference. Thanks a lot. Lalani ''''r In addition: Warning message: In gzfile(file, "rb") : cannot open compressed file '', probable reas…

RNAseq R Atena

updated 3.2 years ago • lalanis1

function in R, but I want to ask you if the matrix should be just normalized with DESeq2 or also log trasformed. I did this passage: ```r dds_campione <- DESeqDataSetFromMatrix(countData=raw, colData=condition_breakfast...matriceFiltrata), gset.idx.list = tebua) ``` Is it ok or I also have to log trasformed the mat…

DESeq2 GSVA ssGSEA

updated 19 months ago • michelafrancesconi8

Corrected array 2 Corrected array 3 Corrected array 4 Corrected array 5 Error in optim(par = c(beta, log(sigma), log(alpha)), fn = normexp.m2loglik, : initial value in 'vmmin' is not finite </div

limma limma

updated 20.5 years ago • Rani Elkon

a matrix of RPKM values: ``` y <- normLibSizes(y) RPKM <- rpkm(y) ``` To make a PCA plot of log-RPKM values ``` logRPKM <- rpkm(y, log=TRUE) plotMDS(logRPKM, gene.selection="common") ``` To make an MDS plot from the log-RPKM values

rpkm edgeR featureCounts

updated 2.4 years ago • Gordon Smyth

Using the web browser to connect to the Rstudio Server's login page on the master node,  after log in with username 'ubuntu' and password 'bioc', i get the rstudio initialization error:  unable to connect to service...permission. On the other hand however, if i connect to any of the worker nodes, i can successfully log in to R-studio server. I also try just bringing up…

starcluster aws

updated 10.3 years ago • hao.lin

bed, "test_xRNA.bed",row.names = F,col.names = F, sep="\t", quote=FALSE) ``` <sup>Created on 2022-07-29 by the \[reprex package\](https://reprex.tidyverse.org) (v2.0.1)</sup> and I want to convert it into a bed file. I try to do it

rtracklayer R bed

updated 3.4 years ago • L

things totally mixed up here. I was thinking that GLM offsets would be positively correlated with log counts. for instance in edgeR, mglmLS.R: mu <- exp(beta %*% t(X) + offset) but it seems offsets from packages EDASeq and cqn are negative...correlated with log counts. for example some poisson data: > n <- 1000 > covariate <- rnorm(n,6,.5) > coun…

GO edgeR cqn EDASeq GO edgeR cqn EDASeq

updated 12.9 years ago • love

c(6,8,9), genesToLabel = g,labelCol="red", labelpch=20,foldLine=2.46,log=FALSE) > plotMAXY(log2(exprs(BSData)), arrays =c(6,8,9),labelpch=20,foldLine=2.46,log=FALSE) > plotMAXY(log2(exprs(BSData)), arrays...c(2,4,5), genesToLabel = g,labelCol="red", labelpch=20,foldLine=2.46,log=FALSE) > plotMAXY(log2(exprs(BSData)), arrays =c(2,4,5),labelpch=20,foldLine=2.46,log=FALSE) &am…

updated 12.8 years ago • abdul rawoof

for one (or more) post-docs to work in my group. Please write to me, with your cv, relevant publications, current interests and potential starting dates. Robert -- +--------------------------------------------------------------------- ------+ | Robert Gentleman phone : (617) 632-5250 | | Associate Professor...fax: (617) 632-2444 | | Department of Biostatistics offi…

updated 21.2 years ago • rgentleman

using conditional quantile normalization to remove gene length bias. This CQN normalization gives me log expression data that includes negatives. I am unable to perform the DESeqDataSetFromMatrix function to begin identifying...differentially expressed genes. Is there a way to identify differentially expressed genes using log expressed data with negative values in DESeq2? Or is there an output fi…

CQN deseq2

updated 6.1 years ago • nicholas.macknight

preformatted">Hi, I was using an older (11/23/04) version of limma package and it worked fine for my log ratio data. I just installed the latest version (2/24/05) but got this error message when I did: > lmFit(data) # data is just a matrix...of log ratios. Error in sigToEnv(signature, fdef) : Trying to get slot "signature" from an object of a basic class ("NULL") with…

limma limma

updated 20.8 years ago • He, Yiwen NIH/CIT

to vsn but customised for Illumina data, and it returns expression values which are already on a log-scale. It is very easy to check for yourself whether the data is on the log-scale or not. Just type summary(exprs(y)) Do the values...vary from 0 to 16 (as for log-data) or from 0 to 640000 (as for raw data)? Let me gently point out that you never did tell us exactly what commands you used.…

Preprocessing probe vsn limma Preprocessing probe vsn limma

updated 18.3 years ago • Gordon Smyth

gt;> >>> I just had another quick question. The targets are >>> ranked by the log-likelihood. Does this mean that the higher the >>> log-likelihood the greater the probability of the gene being a target...or >>> vice versa? Also what does null log likelihood stand for? >> >> Our …

Microarray impute PROcess convert mmgmos puma tigre trigger Microarray impute PROcess

updated 11.9 years ago • Antti Honkela

argument in the `` gsva() `` function. After carefully examining all related documents (original publication by Hanzelmann et al., package vignette, as well as source code), it appears to me that `` gsva() `` function in its current...f(x) }, sample.idxs)) gene.density <- log(gene.density / (1-gene.density)) } return (gene.density)  <strong># the authors ref…

GSVA gsva abs.ranking

updated 8.7 years ago • sina.nassiri

Hello Everyone, I am trying to construct a GatingSet and apply it to a few samples. I have difficulties getting the gates to end where they should. In particular I often find the CD8+ gate being utterly wrong (see the attached bitmap). Is there any way I can modify things so the gates end up in a more correct place? I would also like to gate on CD45, but so far the only thing I can get working …

opencyto gating

updated 9.7 years ago • Ulrik Stervbo

it as an offset (representative code below). ```r model <- glm.nb(counts_gene_A ~ group + log(gene_A_contamination) + offset(log(library.size)), data) model_offset <- glm.nb(counts_gene_A ~ group + offset(log(gene_A_contamination...offset(log(library.size)), data) ``` Doing this I see very little change in aic values, though `model` usually has a slightly lower aic than...express…

DESeq2 glmGamPoi offset edgeR scRNAseq

updated 18 months ago • Alec

significant whereas the other might not. So I came up with this idea. First I can paste the two log ratio matrices together as follows; ID replicate1 replicate2 ... replicateN A1 logRatioA1.1 logRatioA1.2 ... logRatioA1.N...logRatioB2.N .... B10,000 .... Then, for an ID that occurs in both A and B, take the mean of two log ratio values. For example, if A1 and B1 correspond to the same …

Microarray probe Microarray probe

updated 17.4 years ago • Seungwoo Hwang

0 0 0 0 0 1 0 0 0 0 0 0 1 0 But somehow I can neither create it nor write the right header. I would appreciate your help Thanks Assa [[alternative HTML version deleted]] </div

updated 14.0 years ago • Assa Yeroslaviz

to create the annotation package for GPL10427. It is ovine species platform, and there is no .db0 nor schema for it. I'm trying to read 'Creating an annotation package with a new database schema'. It's ashamed of me, but I'm an R beginner

Annotation hgu95av2 Annotation hgu95av2

updated 12.3 years ago • Guest User

Have run into an error when using genefilter to run a t-test. Error seems to indicate genefilter is nor recognizing format of eset. Please advise. Thanks again. > data AffyBatch object size of arrays=1164x1164 features (42346

cdf genefilter cdf genefilter

updated 21.2 years ago • rkakkar@uchicago.edu

ok Error in missing(affy.attr) : 'missing' can only be used for arguments but neither in the help nor in the function parameters there is one called affy.attr. I checked the function and there is a call to limma2biomaRt.n

affy affy

updated 18.2 years ago • Mayte Suarez-Farinas

have done to these data. 1. Normalized data means they are preprocessed and normalized, if they are log transformed? 2. If I want to zscore transform the normalized data, if I should do log transformation first? 3. In addition, illumina

Microarray PROcess Microarray PROcess

updated 15.3 years ago • Zhe Liu

library(edgeR) cts <- txi$counts normMat <- txi$length normMat <- normMat/exp(rowMeans(log(normMat))) library(edgeR) o <- log(calcNormFactors(cts/normMat)) + log(colSums(cts/normMat)) y <- DGEList(cts) y$offset <- t(t(log(normMat

tximport edger

updated 7.9 years ago • Xiang Wang

avgTxLength"]] #transcript length matrix norm.mat <- transcript_lengths / exp(rowMeans(log(transcript_lengths))) #divide out geometric mean #from estimateNormFactors: sf <- estimateSizeFactorsForMatrix(counts_dds...factors and size factors are multiplied normalization_factors <- nf / exp(rowMeans(log(nf))) # normalization factors are still normalize…

normalization deseq2 across species rnaseq

updated 5.6 years ago • rmurray2050

my perspective as a relative newcomer into this field. At first I too was alarmed by the apparent violation of statistical orthodoxy involved in pre-filtering. But after witnessing how well this works on real data, my opinion

Microarray Microarray

updated 17.5 years ago • Assaf Oron

Type 'contributors()' for more information and 'citation()' on how to cite R or R packages in publications. Type 'demo()' for some demos, 'help()' for on-line help, or 'help.start()' for an HTML browser interface to help. Type 'q()' to quit...lt;- estimateTagwiseDisp(DGE_List_Object) > > # Plotting tagwise dispersion estimates against log- concentration(i.e. tag abundance) > …

Normalization limma edgeR Normalization limma edgeR

updated 13.7 years ago • Javerjung Sandhu

for task: 593957982 building: Parsing manifest ################################ Begin Task Log ################################ ################################# End Task Log ################################# Error: Unhandled Exception: Child Task 593957983 failed: Error parsing manifest: Unable to determine package

software error

updated 6.8 years ago • sqz986536

with mix of apple and oranges, and there are 10 such tables (T1 to T10. Now, I have computed the log-odd score of finding apples in B1 at all 10 tables: <pre> 2.95 5.56 6.025 7.225 7.37 7.39 7.54 7.54 6.82 7.295</pre> To generate...and B2 on every table, keeping the number of fruits in each basket same as above. And again computed log-odd score of fin…

statistics hypotheses R

updated 9.8 years ago • Bade