Bioconductor Forum

and I also looked through the issues on github, but I still don't understand how MAST calculates log fold-change. According to this documentation [https://rdrr.io/bioc/MAST/man/logFC.html][1], the log fold change from contrast0

MAST

updated 3.4 years ago • Chenghao

Steps to reproduce: "log in" -> "with StackExchange ID" -> (log in to your account) -> (approve permission) After that there is an error message giving

website

updated 10.0 years ago • balwierz

community? Nominate for the New Contributions to Bioconductor Award! Nominations are open to the public and the deadline is May 20, 2022. Please fill out this [Nomination Form](https://forms.gle/u7iWAiRUYaB8pR4H8) and be sure

Recognition Awards Bioc2022 Bioconductor

updated 3.7 years ago • shepherl

class="preformatted">Dear bioconductor, I just asked myself if the values returned by justPLIER are log-base 2 oder 10? Can I change the base? What is the default? Thanks in advance, Andreas Heider [[alternative HTML version deleted

updated 14.7 years ago • Andreas Heider

I am a new learner of DESEQ2 and have seen similar posts on this forum but could not find clear answers. What would be the best way to create heatmaps specifically with 2 log fold change(base 2) in DESEQ2 or R in general? In DESEQ2, heatmaps are created based on VST (Variance Stabilizing Transformation) values. The count data I've used is unnormalized raw counts from FeatureCounts. I would…

DESeq2

updated 2.5 years ago • bio2249

of 6. Does that mean to calculate the fold change you would do 2^6 = 64 ?Therefore the gene has a log fold change of 64

DESeq2

updated 4.2 years ago • adeler001

Hi, from what I understand then (note: this is a follow up to a question asked on the tximport github) the cpm counts calculated in the last line of the tximport edgeR vignette, that is: ``` cpms <- edgeR::cpm(y, offset = y$offset, log = FALSE) ``` cannot be used directly (I mean as they are) to calculate logFC between expression levels of a gene of interest in two... Hi, …

tximport

updated 4.1 years ago • mailmpunta

geometric average, and not to the ratio itself (without the logarithm). As in: <pre> exp(locfunc((log(cnts) - loggeomeans)</pre> and not: <pre> locfunc(exp((log(cnts) - loggeomeans)</pre> I've been following your publication (Anders, Huber

deseq2 normalization

updated 9.6 years ago • lapinskim

it is specifically written "Kanehisa Laboratories". Is it a problem, or are these figures free for publication ?    thanks a lot Assaf &nbsp

pathview clusterprofiler

updated 9.3 years ago • assaf www

div class="preformatted">Hi All: Even after going through hand full of posts on log fold change, I could not figure out how exactly it is calculated in LIMMA. Please see following example. Arrays 3 and 4 are

limma limma

updated 15.8 years ago • Jay

div class="preformatted">Hi, I have a microarray dataset from Agilent chips. The data were really log ratio between test samples and a universal reference RNA. Because of the nature of log ratios, coefficient of variation...CV) doesn't really apply to this kind of data due to the fact that mean of log ratio is very close to 0. What kind of measurements would people use to measure the dispersio…

Microarray Microarray

updated 13.9 years ago • array chip

employed 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 the assumptions

updated 15.0 years ago • r_1470

if the dependent variables in edgeR and limma should be used as a raw measurements or should they be log transformed if they are skewed

limma edgeR

updated 5.2 years ago • anna.cot.anna.cot

The log function seems to not be working correctly when ramwas1scanBams(param) is called. This code snippet might be a good way...Parallel job function # .ramwas1scanBamJob = function(bamname, param){ # ld = param$dirfilter; # # .log(ld, "%s, Process %06d, Starting BAM: %s", # date(), Sys.getpid(), bamname); # # rez = pipelineProcessBam(bamname = bamname, param = param);…

log timer

updated 2.9 years ago • Anushka

preformatted">Hi All. Apologies as I'm just getting to grips with R. I have a set of genes and log fold changes. As the genes have been converted from Affymetrix probes, and up to 11 probes represent one gene, I have a range...of different log fold changes for each gene. I would like to take the average log fc for each gene when duplicated in the list. I used the script

updated 12.4 years ago • Helen Smith

a design matrix that can identify differentially expressed loci - for example conducting a log ratio test to see if the duplicate factor is significant in the design. My question is whether this violates assumptions

rnaseq DESeq2

updated 2.1 years ago • pl23

the gene-specific UMI counts by the median number of UMIs obtained from each cell, and taking the log-transformation of the gene/cell matrix (this all seems very similar to what we would do with RSEM or EdgeR). From my perspective...to the UMI approach, the 5'/3' specific sequencing, or this particular normalization approach) violate assumptions underlying the MAST framework.  Thanks f…

MAST mast dropseq

updated 7.9 years ago • jeremycfd

The Department of Experimental and Health Sciences ([DCEXS][1]) of the Universitat Pompeu Fabra ([UPF][2]) aims to fill two Tenure-Track Group Leader positions in the fields of Computational Biology and Biological Chemistry. We encourage applications from outstanding scientists working in any area within these two fields. These include, but are not limited to, in the case of computational biology…

bioinformatics genomics proteomics biologicalchemistry sequencing

updated 4.0 years ago • Robert Castelo

code><strong>Following code shows that "log(imageData, base=2)" is broken.  Could it be fixed?  Thanks!!</strong></code>   <code><span style="line-height:1.6">> library...nbsp;186<br/> [5,]  184  185  186  196  179  182</code> <code>> log(image.data…

bug ebimage

updated 10.2 years ago • feimingc

Hi Everyone,  I am running a rna seq differential gene expression experiment with the following code: <pre> dds <-DESeqDataSetFromMatrix(countData = ep,colData = cp,design =~Age+Gender+Response) dds <- DESeq(dds) res <- results(dds,contrast=c("Response","Yes","No"))</pre> Looking at the results I get about thousands genes with absolute log fold chan…

lfcthreshold deseq2

updated 8.0 years ago • lirongrossmann

oQs5ggMAdZ_QZofs5P3W0g My question is about whether it makes a difference that I'm using the log transformed data? I know that the log transform is not linear, meaning that logged data and raw data will yield different

Clustering Clustering

updated 16.7 years ago • Paul Geeleher

<div class="preformatted">Hi to all, I have a problem that really I cannot solve. Some signal log-ratios given to me converting a RGlist with MA.RG(RG) are different from the ones calculated directly, that's the point: Looking...div class="preformatted">Hi to all, I have a problem that really I cannot solve. Some signal log-ratios given to me converting a RGlist with MA.RG(RG) are d…

updated 20.8 years ago • Giulio Di Giovanni

div class="preformatted">Dear edgeR Users, Is there a possibility to extract the log likelihood values of genes under under GLM approach? Bests, Eszter -- Eszter Ari Institut für Populationsgenetik Vetmeduni

edgeR edgeR

updated 12.9 years ago • Ari Eszter

and I understand that a value of LR = 0 is a 50-50 chance of being a DEG. But is there a posterior log-odds transformation of the LRT (delta-deviance) value that can be interpreted the same way as limma's B score? My back of the...envelop scribble seems to indicate that an LR-based posterior log-odds (given fixed prior proportion p of being a DEG, say 0.01) is: logOdds = logit(p) + LR/2 Yes? …

updated 11.9 years ago • Aaron Mackey

Hello, I'm having trouble finding the height, weight and BMI variables in a public gse73103 database. I was able to import the data with the following code. ```r gse73103<-getGEO('GSE73103') ``` I got this result

GSEABase GenomicDistributionsData

updated 20 months ago • Yveto

comparisons,"-goNodes.svg")) > plot(goNodes) Error in xy.coords(x, y, xlabel, ylabel, log) : 'x' is a list, but does not have components 'x' and 'y' > dev.off() RStudioGD 2 What did I miss? Thank you in advance

topgo svg

updated 8.3 years ago • mictadlo

transcripts were going way down. However, I can't remember what they >advised to do in this case, nor which paper it was - anyone know? > >This situation also turns out to be very similar to the spike-in experiment >of Choe

Microarray Normalization probe limma gcrma Microarray Normalization probe limma gcrma

updated 20.0 years ago • Matthew Hannah

of the lumi package is that it does not directly normalize the data at the M-value level (since it violates the assumption of many normalization methods), instead we normalize the data at probe intensity level. Actually...the adjusted data using Lumi to csv format, so that I could calculate beta_value eventually for publication, my boss asked me to use beta_value as most publication use beta_valu…

Normalization probe lumi Normalization probe lumi

updated 13.8 years ago • Pan Du

<div class="preformatted">Hi, I wish to use R to have the log(2) expressions of genes from a few cDNA samples (from layout: PMCI_10.5KSC_GP.gal). The experiment is done with a common reference...div class="preformatted">Hi, I wish to use R to have the log(2) expressions of genes from a few cDNA samples (from layout: PMCI_10.5KSC_GP.gal). The experiment is done with a common

updated 16.7 years ago • santana sarma

is up to date. My problem is I can’t use the function “getBM” in all of the ways. The error log is "Error in loadNamespace(name) : there is no package called ‘withr’ ”, which I can’t found the package “withr” to support this function

biomaRt annotationTools

updated 5.0 years ago • niyamurry

preformatted">Dear Bioconductor users, I have been assuming that the base of the B-value log in Limma = 2, but I recently reread the paper and didn;t see a base. Is the base 2, and if not what is it/ Thanks and best wishes, Rich

Cancer limma Cancer limma

updated 8.5 years ago • Richard Friedman

HSMMSingleCell is the most popular RNASeq dataset in the Bioconductor ExperimentHub as of early 2022. The vignette information talks about how the sequencing was performed and expression calculated, but there are several...that also basically correlates with timepoint, but no explanation of what it is. Is there a publication for this dataset? It's a few years old, but top ranked in rna…

ExperimentHubData ExpressionData CellDataSet RNASeqData

updated 3.8 years ago • karl.stamm

parameter" in DESeq2, is that referring to the parameter "r" or the parameter "alpha" in the wikipedia page? They're reciprocal to one another, and either one can be called the "dispersion parameter" depending on context

deseq2

updated 5.8 years ago • stephen.hartley

I play with the lfc argument in the treat function I get different results. I do not know what the log fold change corresponds in my case? Any help is appreciated Thanks

limma multiple factor design

updated 10.6 years ago • ea1402

branch. As I cannot reproduce the error on my own computer I wanted to have a look at the error log that exists from the CHECK report on Bioconductor devel branch. Can anyone tell me how I access the error log file on the

build testthat cmd check

updated 10.2 years ago • Peter

provides one that smoothly interpolates between the square- root function for low counts and the log-transformation for higher counts, see Section 6 (and 7) of the vignette. Best wishes Wolfgang Il giorno Jan 31, 2013, alle ore...I would > especially value Gordon and Charity's comments if they have time. > > The voom log transformation is essentially: &g…

limma edgeR DESeq limma edgeR DESeq

updated 12.9 years ago • Wolfgang Huber

testing in RNAseq data. Should I obtain the principle components on the raw counts or following log adjustment? thanks. myData <- myCountTable logMyData = log(myData + 1) ruv1 = svd(logMyData - rowMeans(logMyData))$v\[,1\] ruv2 = svd(logMyData

deseq2 rnaseq normalization

updated 10.2 years ago • rowleyrolls

exprs(eset.mas5)#to get the expression matrix (probesets/genes in rows, chips in columns). exprSet = log(exprSet.nologs, 2)# to transform in log2 the absolute gene expression summarized values. Now the point is: after log2 transformation

Microarray Normalization simpleaffy Microarray Normalization simpleaffy

updated 13.8 years ago • Guest User

Hi Bioconductor Team! Can regularized log/rld transformed values of 16S microbial taxon abundances be treated as independent of each other? Or are the resulting

deseq2

updated 5.7 years ago • mtswanson2017

div class="preformatted">Hello Arne, Several publications recently have shown that the distribution of gene abundances seems to follow a power law (one such is referenced...at www.the-scientist.com. This should turn into an exponential density on the log scale we often use. The 'hump' we see in signal intensities from microarray experiments probably reflects variable levels

probe probe

updated 21.9 years ago • Mark Reimers

div class="preformatted">Hi Bioc I am using cph in the library Design so that I can compare the log likehood ratio test for different nested cox models. I am testing about 50 genes. Whilst I can use p.adjust to correct for...I can apply? Or can I modify this for cph? Thanks Aedin -- Aed?n Culhane Harvard School of Public Health, Dana-Farber Cancer Institute </div

Cancer Cancer

updated 17.7 years ago • Aedin Culhane

Two tools give the adjusted p-values for multiple testing.  DESeq used Benjamin-Hochberg correction and edgeR uses FDR. According to wikipedia Benjamin-Hochberg is the same as FDR. So, the correction is the same, but the names are different, right? Also, how do those...multiple testing.  DESeq used Benjamin-Hochberg correction and edgeR uses FDR. According to wikipedia …

deseq2 edger

updated 10.2 years ago • tonja.r

cl, logged=TRUE, rand=123) Because the user guide mentioned the data of dual microarray inputted as log-scaled fold-change (FC) ratio, I prepared the data set of log-scaled FC, but the RankProd just calculated the average FC as (sum...of all log-scaled ratio)/4. The log-scale did not considered. Therefore, my question is: 1. The data set of dual channel microarray must...to use the transformed…

Dual channel microarray Rankprod

updated 8.9 years ago • ggyu1215

the data, some of the three replicates of one gene are all 0 reads count, why it still can be count log 2 fold change, or I misunderstood something

DESeq2 RNASeqData

updated 3.8 years ago • YATING

I use normal workflow for Agilent microarray data. So, I just want to ask how can I get a matrix of log transform of RNA-seq values and microarray intensities using Limma? I expect the result would be like a matrix with columns

limma

updated 10.1 years ago • bharata1803

in section 2.1.1 about the appropriateness of setting the blind argument when performing regularised log transformation. Specifically, the comment that ?...blind dispersion estimation is not the appropriate choice if one expects

Clustering DESeq2 Clustering DESeq2

updated 11.9 years ago • Mike Stubbington

<div class="preformatted">Hi fellow ComBat fans, Not sure if my previous message posted to the listserv because of the attachment. Now re-sending without attachment: I was having a problem with ComBat when using large batch sizes and the non-parametric parameter estimation. Almost all probe intensity values after ComBat correction would be NAs. I've traced the source of this problem an…

probe probe

updated 7.8 years ago • Jason Stein

is a great place to get help: https://stackoverflow.com/tags/shinyjs R version 4.1.3 (2022-03-10) -- "One Push-Up" Copyright (C) 2022 The R Foundation for Statistical Computing Platform: x86_64-apple-darwin17.0 (64-bit...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…

igsva GSVA

updated 2.9 years ago • sharvari gujja

with *scaling* parameter `(s_0)^2`. In that case, the mean is `d_0 * (s_0)^2 / (d_0 - 2)` (see [Wikipedia][1]). So my question is: Am I right that the correct mean for the prior of the `(sigma_g)^2` is `d_0 * (s_0)^2 / (d_0 - 2)` and not `(s_0)^2` ? [1]: https

limma

updated 6.4 years ago • Homer

to brain weight and would appreciate feedback to make sure I'm not doing anything that would violate DESeq2's internal modeling. I perform the following steps: 1. Collect Conditional quantile normalization (CQN) for...brain.weight/1000) # Divide by geometric normFactors.bw <- cqnNormFactors.bw / exp(rowMeans(log(cqnNormFactors.bw))) dds <- DESeqDataSetFromMatrix(countData…

deseq2 cqn normalization normalized counts

updated 8.2 years ago • mark.ebbert

a sanity check. I would especially value Gordon and Charity's comments if they have time. The voom log transformation is essentially: log2( (count+0.5) / library.size ) It then does some clever things with weights. What I'm considering

limma safe edgeR limma safe edgeR

updated 13.0 years ago • Paul Harrison

helpful for our analysis.     May I ask you whether it is possible to report also the log normalized read counts (used for the seqplot function) as .csv table similar to the functions:   > segm <- as.data.frame

cn.mops log normalized counts table

updated 8.5 years ago • falk.zakrzewski

Hello to everyone, I've followed the "A step-by-step workflow for low-level analysis of single-cell RNA-seq data with Bioconductor, V2" for my own data. The problem is that when I produce the graph for Variance of normalized log-expression values (using trendVar and decomposeVar functions), my plot (an ascending-linear shape in which all of dots...V2" for my own data. The problem is tha…

workflows simplesinglecell

updated 7.3 years ago • es.azadian

gt; Subject: [BioC] [ComBat] ComBat outputting NAs with Large Batches - > Switch to Log Likelihood > Message-ID: <20121121110033.256149mixyg20d75 at mail.ucla.edu> > Content-Type: text/plain; charset...in a batch or when there are > large residuals (or both). To correct this, can use the > log-likelihood, which is less susceptible to numeric…

probe probe

updated 13.1 years ago • W. Evan Johnson

1.4-5 2016-07-21 [1] CRAN (R 4.2.0) AnnotationDbi * 1.58.0 2022-04-26 [1] Bioconductor AnnotationHub * 3.4.0 2022-04-26 [1] Bioconductor ape 5.6-2 2022-03-02 [1] CRAN (R 4.2.0) aplot 0.1.6 2022-06...1] CRAN (R 4.2.0) magrittr 2.0.3 2022-03-30 [1] CRAN (R 4.2.0) MASS …

clusterProfiler

updated 3.5 years ago • Y.K

everyone,   I have just read the vignette about DESeq2 and I have a question about shrunken log fold changes and threshold test. I use DESeq() and results() functions to get the gene set with absolute LFC > 1. I understood

deseq2 lfcshrink lfcthreshold differential gene expression

updated 7.1 years ago • corentinrichard374369

extracting non-logged form of data for downstream analysis however I could extract the normalized log-intensities for both arrays, How do I obtain unlogged normalized values. Which one of the below function seems appropriate

IlluminaChip limma AffymetrixChip Normalization Microarray

updated 2.8 years ago • Abdul

Good morning, I am trying to understand the relative log expression normalizat ion made by the DESEQ2 wrapper function. As far as I understood, It corresponds to the computing...of the j-th sample's counts to those of the pseudo-reference."_   _But there is non log transformation in that formula so I'm not sure it is the right description of the RLE normalization method._ …

rle deseq2 normalization

updated 7.6 years ago • Aurora

preformatted"> Hi! We selected a priori 5 genes to analyse and want to include them in a table for publication. Question is how to present them? Normally we would calculate fold changes (or percent) with standard deviation

updated 12.0 years ago • Guest User

Moderna is hiring a statistical genomics co-op in 2022 to work on single-cell genomics applications for immunology research (masters or PhD with experiences in single-cell

co-op immunology single-cell omics

updated 4.3 years ago • joyce.hsiao1