Bioconductor Forum

Hello everyone, I thought of conducting a parallel DE analysis with EdgeR and DESeq using a dataset that I have been working on lately. The dataset has two conditions with two biological replicates each. Let's say: Wild Type, Wild Type, Knock Out, Knock Out. It's a smallRNA-Seq dataset, mapped to miRNAs. I have tried various analyses using both programs and I have noticed this. There are ve…

Normalization edgeR DESeq Normalization edgeR DESeq

updated 13.1 years ago • Ioannis Vlachos

> plotDensity(log2(raw.data\[,3:8\]+0.1) + >legend(15,0.1,legend=targets$FileName,lty=1:6,col=1:6) + legend(15,0.1,legend=targets$FileName,lty=1:6,col=1:6) Error: unexpected symbol in: ">legend(15,0.1,legend=targets$FileName,lty=1:6,col=1:6) legend" > legend(15,0.1,legend=targets$FileName,lty=1:6,col=1:6) Error in strwidth(legend, units = "user", cex = cex, font =…

limma

updated 10.1 years ago • anu.kour

hi Dario, I CC the Bioconductor mailing list, On Wed, May 7, 2014 at 11:00 PM, Dario Strbenac wrote: > Hello, > > As section 5.3 of the vignette explains, the transformed data can be used for applications like clustering of samples. I was considering the best way to use it instead for clustering genes of a time-series experiment. I would have to account for gene length to make differe…

Clustering DESeq2 Clustering DESeq2

updated 11.7 years ago • Michael Love

I have a metagenomics dataset, which essentially is a counts matrix (genes as rows and samples as columns). One of my objectives was to identify differentially abundant genes across my sample groups, which I did using DESeq2 I am wondering if its also possible to do some qualitative testing, based on the presence-absence of a gene and quantify that using a metric such as the odds ratio?

deseq2 limma

updated 9.3 years ago • adityabandla

Hello, In order to use a model selection approach, I would like to compute BIC or DIC values. Unfortunately, I can't retrieve the LL for my fit. Is there any way I can use the deviance to find it knowing that Residual Deviance = 2(LL(Saturated Model) - LL(Proposed Model)) on df ? But if it's the case I would need the LL for the saturated model and I can't compute it... Best Cédric

edger bic mode selection

updated 9.9 years ago • cedric.gobet

not able to find the R command to obtain the list of Differentially expressed genes at a Fold change (log-fold change) and FDR cut-off

limma

updated 8.9 years ago • ask4arifali

Biology Using Perl and R Gabriel Valiente, Technical University of Catalonia, Barcelona, Spain Publication Date: April 2009 Number of Pages: 368 Emphasizing the search for patterns within and between biological sequences...R Owen Jones, Robert Maillardet and Andrew Robinson, University of Melbourne, Parkville, Australia Publication Date: March 2009 Number of Pages: 472 This book teaches t…

Cancer PROcess Cancer PROcess

updated 16.6 years ago • Calver, Rob

TPM is considered a normalized metric and I have seen plots of TPM in papers before (typically as log TPM). I was re-reading the DESeq2 manual and found a post on here that recommended using counts(dds,normalized=TRUE). I wanted...library size? In that case, if I wanted to calculate mean TPM of a gene and visualize expression (log TPM) via box plot, that I should use the counts(dds,normaliz…

DESeq2

updated 23 months ago • mp52226

Hi David Yes, the logFC values given in edgeR are the log2 fold changes. To get the non-log FC it is just 2^(logFC). Best regards Davis --------------------------- Original Message ---------------------------- Subject: [BioC] edgeR From: "David martin" <vilanew@gmail.com> Date...the edgeR package fold changes rare given as logFC. Is that the log2 value ? how can i get the non log FC ?…

edgeR edgeR

updated 15.6 years ago • Davis McCarthy

div class="preformatted">Dear all As we know a median normalization shifts the center of the log-ratio distribution to zero but does not affect the spread. when i plot a density plot after median normalization, impact...normalizeWithinArrays(RG,method="none") M1=MA$M plot(density(M1,bw=0.17),main="density plots",xlab="log ratios", ylab="density",col=1,lty=1,lwd=3) MA=normalizeWithinArrays(RG,m…

Normalization Normalization

updated 14.6 years ago • samane fazeli

loess in this case) re-normalized using Aquantile? Since the idea of using Aquantile is so that the log ratios are not changed but the samples are adjusted to have the same distribution of A values, my concern is that by using...a 1st step of normalization the log-ratios do not remain untouched. Does the guide mean to do the following: MA <- normalizeBetweenArrays(RG, method="Aquantile

Normalization limma Normalization limma

updated 14.3 years ago • Hari Easwaran

expressed. But I am not able to separate the gene list that is up regulated (+ve LogFC - log Fold change) and down regulated  (-ve LogFC - log Fold change) from the significantly differentially expressed using

edger R Up reg genelist

updated 7.6 years ago • drskm7

__General Description:__ A post-doctoral position is available to develop methods and data resources for R / Bioconductor to integrate complex, heterogeneous, and large cancer genomic experiments. This National Cancer Institute-funded project is a collaboration between Bioconductor team members at Hunter College (a senior college of the City University of New&nbs…

bioconductor New York Job

updated 11.1 years ago • Levi Waldron

The Institute of Medical Biostatistics, Epidemiology and Informatics ([IMBEI](http://www.unimedizin-mainz.de/imbei/)) at the University Medical Center, is seeking a motivated __Bioinformatician/Statistician (m/f) __ - Reference 50028764 The Division Biostatistics/Bioinformatics coordinates various biostatistical/bioinformatic supporting activities, covering a broad spectrum of studies. Over the…

rnaseq biostatistics bioinformatician next-generation sequencing Job

updated 8.0 years ago • Federico Marini

FindIntegrationAnchors) and later for the integration, PCA, UMAP, clustering, etc. I am using log normalized and scaled data. I am using this code to perform analysis. ``` integration.features <- SelectIntegrationFeatures...lt;- FindClusters(integrated.data, resolution = 0.5, verbose = T) ``` When I am using linear log normalization for both anchors detection and integration, ther…

Normalization scRNAseq

updated 3.8 years ago • nitinnarwade1504

all(rownames(coldata) == colnames(cts)) dds <- DESeq(dds) Next I plot the deviance vs. log of mean expression (base mean). Both are contained in the data frame returned by `mcols`. mc = as.data.frame(mcols(dds)) plot(log...mc$baseMean), mc$deviance) The plot shows a fairly linear increase of deviance with log of the mean expression. From my somewhat limited understan…

deseq2

updated 6.9 years ago • Peter Langfelder

<div class="preformatted">limma allows you to normalize on any set of control spots using any of the normalization methods "loess", "printtiploess", "robustspline". See page 15 of the User's Guide. (Although I don't actually recommend this with spike-in controls, because of the risk of systematic bias in spike-in volumes relative to sample volumes.) The technique is simply to set up a vect…

Normalization limma Normalization limma

updated 20.5 years ago • Gordon Smyth

counts for some genes are not consistent with their TPM. Then we checked the correlations between log-transformed TPM and normalized counts based on 2-factor, and the correlation for single sample based on expressed genes...single sample][1] while the correlation for the ratio of each group, for example, correlation of log( normalized counts of (patient-stimulation 1/ctrl-stimulation 1) ) and lo…

DESeq2 RNASeq

updated 4.7 years ago • hequn

<div class="preformatted">(Please cc me on replies, as my mailing list subscription request doesn't seem to have been processed yet.) Hi All, Couple of web site comments: 1) The current layout of the bioconductor.org doesn't provide much guidance to getting started with the bioconductor packages. There is no clear links to documentation and no introduction to the tools. Would it be pos…

Biobase edd ROC Biobase edd ROC

updated 23.6 years ago • Warnes, Gregory R

s1, s2 , type = "global") pattern(algmt) aligned(pattern(algmt)) Neither pattern(algmt)  nor   aligned(pattern(algmt))   return the global alignment of the two sequences if there are gaps on either

biostrings alignment

updated 9.2 years ago • map2085

I’m experimenting with the ability of fry/mroast functions to include gene weights. I have two use cases:   __1) Comparing the result of a previous experiment in mouse, with a current experiment in human: __Basically I want to see if a previous observed response in mouse is observed in a similar human experiment. I can use Ensembl homologs to match results from the mouse data to the hu…

limma mroast fry

updated 7.3 years ago • maltethodberg

its utility. Thanks, --t *He that would live in peace and at ease, * *Must not speak all he knows, nor judge all he sees.* Benjamin Franklin, Poor Richard's Almanack<http: archive.org="" details="" poorrichardsalma00franrich

RNASeq qPCR affy oligo frma RNASeq qPCR affy oligo frma

updated 12.2 years ago • Tim Triche

But when I use the GLM approach, I cant find them (neither the information in the documentation nor the counts in any object produced). Where are they stored ? For information, here is the sessionInfo() and maintainers: > sessionInfo

edgeR edgeR

updated 11.8 years ago • Mathieu Bahin

Hi I have been trying to install SeqArray however I have been having the same problem with the ‘GenomeInfoDbData’. Somebody could help me please, I already restart R, I have the last version, but I really dont understand what is happening. bellow the code and the error: ``` if (!require("BiocManager", quietly = TRUE)) install.packages("BiocManager") BiocManager::install("SeqArray") library(S…

Install

updated 3.7 years ago • laiajulianamu

https://ftp.osuosl.org/pub/cran Bioconductor version 3.14 (BiocManager 1.30.16), R 4.1.3 (2022-03-10) Installing package(s) 'BSgenome.Hsapiens.UCSC.hg19' installing the source package ‘BSgenome.Hsapiens.UCSC.hg19

BSgenome.Hsapiens.UCSC.hg19

updated 3.8 years ago • Bogdan

mirrors.tuna.tsinghua.edu.cn/CRAN/ Bioconductor version 3.14 (BiocManager 1.30.16), R 4.1.3 (2022-03-10) Installing package(s) 'org.Hs.eg.db' 安装源码包‘org.Hs.eg.db’ trying URL 'https://bioconductor.org/packages/3.14/data

org.Hs.eg.db

updated 3.7 years ago • yt_lei1998

the form at [https://forms.gle/FDNsHvoMh8AtR9BHA][2]. Applications close on Friday 25th February 2022. New members will be elected from the submitted list of nominations by the current community advisory board members

bioconductoroversight community CAB

updated 4.0 years ago • shepherl

Is there any documentation on statistics used in limma package? How should limma be cited in a publication. Thanks Sohail Khan Scientific Programmer COLD SPRING HARBOR LABORATORY Genome Research Center 500 Sunnyside

limma limma

updated 20.8 years ago • Khan, Sohail

cooksCutoff=FALSE`. How should I solve this? Any suggestion which one I should represent for a publication-ready plot

deseq2 pvalue lfcshrink

updated 6.8 years ago • peibo_xu

documentation shine! Nominate someone for outstanding documentation. Nominations are open to the public but the deadline is fast approaching. Please fill out the [Nomination Form](https://docs.google.com/forms/d/e/1FAIpQLSdaI6KHsezSQLWcCAzRCLlOz_fJai59PcyIz03ifutbwmXaVw

bioconductor bioc2020 award recognition documentation News

updated 5.6 years ago • shepherl

<div class="preformatted">This is the first time I am asking question on Bioconductor and I am not sure which address I should be emailing to. Hope I didn't send to the wrong address. Hi I am using LimmaGUI at the moment to analyse quite a large dataset which includes lucidea spiking controls. I realise that when I used LimmaGUI to plot MA plot on individual slide with coloured legend, ev…

limmaGUI limmaGUI

updated 20.8 years ago • Choon Wei Wee

Dr. Reinhard Hoffmann Email: r_hoffmann at m3401.mpk.med.uni-muenchen.de -----BEGIN PGP PUBLIC KEY BLOCK----- Version: PGP 8.0.1 - nicht f?r kommerzielle Nutzung lizenziert: www.pgp.com mQGiBEBiqn0RBADD7cwc5NHH98xZUn0hG53uL1nw2aVRXwurSWjqK5ytCUh2ZqB4...8VDwCgq/2PAsRp0rAX iXS1T2bL7Fow9zUAnAtzantYb0tV+Iw603AsKQjyDPBW =LGSI -----END PGP PUBLIC KEY BLOCK----- </div

probe probe

updated 20.2 years ago • Dr. Reinhard Hoffmann

name' column. I suspect that summarizeToGene make some sort of assumption about the txid that I am violating. ``` grep ENST00000456328 gencode.v35.ucsc.rmsk.tx.to.gene.csv ENST00000456328.2|ENSG00000223972.5|OTTHUMG00000000961.2

sumarizeToGene tximport

updated 5.0 years ago • aedavids

I would like you to tell me why the filtered expression matrix M should log-transformed after adding a pseudo-count of 1: M’ = log2(M + 1). Thank you

SC3

updated 7.5 years ago • liushang

Hi, this question relates to post [Time-course, comparison of two groups][1]. I have different question related to the data presented there so I've made new question. I'd like to plot observed and fitted log-CPMs for a selected gene or genes. I've consulted `edgeR` user guide (p. 113, the bottom block of code). But there is plot for one time...related to the data presented there so I've made n…

timecoursedata edgeR

updated 2.8 years ago • boczniak767

<div class="preformatted">Pedro, > I do not know if there is any forum where to ask people or > share experience about this package. The best place to discuss affylmGUI is on the Bioconductor mailing list: http://www.bioconductor.org/mailList.html https://www.stat.math.ethz.ch/mailman/listinfo/bioconductor I hope you don't mind that I've copied my reply to the mailing list,…

Genetics affylmGUI limmaGUI convert Genetics affylmGUI limmaGUI convert

updated 21.6 years ago • James Wettenhall

understanding both `cqn` and `EDASeq` return offsets that are of the following form: ``` offset = log(normed_counts) - log(actual_counts) ``` See page 4 of [cqn vignette](https://bioconductor.org/packages/release/bioc/vignettes

DESeq2 cqn EDASeq

updated 4.7 years ago • Saulius

order them by increasing concentration, and transform both the concentration and intensity by log base 2, I see a nice sigmoid curve that I can fit with a cubic polynomial. However, when I pull out the ERCC controls after summarization...when I reorder by concentration, and roughly calculate the log-fold change they are all close to 1?? My supposition is that I am overfitting the data with RMA a…

Normalization xps Normalization xps

updated 11.5 years ago • Matthew Thornton

amp;& (is.null(offset) || max(offset) == -Inf)) { abundance <- rep(-log(nrow(y)), nrow(y)) return((abundance + log(1e+06))/log(2)) } } if (is.null(dispersion)) dispersion <- 0.05 isna <- is.na(dispersion) if (all(isna

edgeR

updated 2.5 years ago • Josué

for the ERCC probes from both groups across my samples 3 treatments and 1 wild-type. When I graph 2 log concentration versus 2 log intensity, I get a sigmoid curve, with a linear region between a 2 log intensity of 6.5 to 10.5

Normalization vsn graph Normalization vsn graph

updated 12.0 years ago • Matthew Thornton

div class="preformatted">Dear listers: I searched the literature and failed to find some public tools used for biclustering analysis in microarray application. I am wondering if there is one in bioconductor or

Microarray Microarray

updated 19.3 years ago • Weiwei Shi

Public Service Announcement** - Bioc2019 NYC registration has been very strong and we will likely have to close registration

conference bioc2019 News

updated 6.6 years ago • Levi Waldron

gt; scatter plots. In the above situation, they lie in a region where > FS=32000?10000 and log??(SS)=2.8?0.5. However, the values in the > covariance matrix don't match the dimensions; is there any explanation > regarding...rleigh/ > `. `' Printing on GNU/Linux? http://gutenprint.sourceforge.net/ > `- GPG Public Key: 0x25BFB848 Please GPG sign you…

convert flowCore convert flowCore

updated 15.3 years ago • Josef Spidlen

summary data > flush.console() NULL > BSData39ABC <-createBeadSummaryData(BLData39ABC,log=FALSE,n=3,imagesPerArray=2) > BSData39DEF <-createBeadSummaryData(BLData39DEF,log=FALSE,n=3,imagesPerArray=2) > &gt...Tennis Court Road, Cambridge CB2 1QP Tel: 01223 333331 and MRC Biostatistics Unit Institute of Public Health, Robinson Way, Cambridge CB2 0SR T…

geneplotter affy affyio beadarray quantsmooth beadarraySNP geneplotter affy affyio

updated 18.4 years ago • Krys Kelly

I filled in google form and submitted my svn id and github id to Bioconductor for transitioning svn to git. I got the email that said they got my form. However, I still can't access after 3 days. I'm not sure to whom I need to contact to know my account is authorized or not. Anyone has any suggestion? Thanks.

bioconductor

updated 8.4 years ago • mnchoi67

the bumphunter output be greater than 1 or less than 0 if beta values range from 0 to 1? Is there a log transformation taking place at some point?  Thank you

minfi bumphunter

updated 4.7 years ago • src3

the edgeR package fold changes rare given as logFC. Is that the log2 value ? how can i get the non log FC ? is that 2^(logFC) ? thanks </div

edgeR edgeR

updated 15.6 years ago • David

i.e. Normalized). If you do not log2(x+1) transform the data you will have meaningless estimates of log fold change since the data are assumed to be on the log scale." There are multiple questions in the same thread about what

SCTransform MAST

updated 15 months ago • james.watson1

Hello, So, I use voom/limma workflow to analyse my RNA-seq data. Now, I want to do further analysis, like measuring genes correlation and try some machine learning method (regression, random forest, etc.). My question is, is the output of voom step can be used for this kind of analysis? The voom step I mean is like below: dgeList<-DGEList(readCountClean) dgeList<-calcNormFactor…

limma voom rnaseq

updated 10.0 years ago • bharata1803

Hi, This is an example of reading TCGA-LAML data from maftools. Here is an example from "?maftools". ''' laml.maf = system.file('extdata', 'tcga_laml.maf.gz', package = 'maftools') laml.clin = system.file('extdata', 'tcga_laml_annot.tsv', package = 'maftools') laml = read.maf(maf = laml.maf, clinicalData = laml.clin) ''' This example worked well. I want to analyze melan…

TCGAWorkflowData

updated 3.5 years ago • Y

the form at [https://forms.gle/FDNsHvoMh8AtR9BHA][2]. Applications close on Friday 25th February 2022. New members will be elected from the submitted list of nominations by the current community advisory board members

bioconductoroversight community CAB

updated 3.9 years ago • shepherl

about "CV of replicates" I meant the standard deviation of their log-ratios. However, in his mail Jakob refered to "CV of log-ratios", and you are absolutely right - these are not appropriate. Best...as I > know) standard deviation divided by mean, so it is scale-invariant, i.e > dividing all log-ratios by 2 shouldn't make a difference. It is not > location-invaria…

Normalization Normalization

updated 20.6 years ago • Sheetal Bhan

<div class="preformatted">Hi Firstly, I think limma is excellent and use it a lot, but some recent results are a bit, erm, disappointing and I wondered if someone could explain them. Basic set up was a double dye-swap experiment (4 arrays) involving different animals, one infected with one type of bacterium and the other a different bacterium, compared to one another directly. I used lim…

limma limma

updated 21.4 years ago • michael watson IAH-C

<div class="preformatted">Hi Gordon, I used to use predFC() to get modified log count-per-million values per sample but now I'm switching to cpm(). I just realized that predFC() doesn't use the normalization factors in the DGEList object when design=NULL, but it does appear to use them when the design is specified (see example below) and there is no argument to specify them, unlike cpm(). …

Normalization Normalization

updated 12.4 years ago • Jenny Drnevich

like to install R packages. But I failed. I suspect it has something to do with my inability to log in to https://mghp.osn.xsede.org/. It took me a whole day to solve the problem. Looking forward to your reply

GenomeInfoDbData genomeinfodbdata

updated 2.4 years ago • 15753563659

hi i have downloaded miRNA-seq RPKM-log data from TCGA portal. If i want to find the differentially expressed miRNA , can i used directly RPKM data or do i need to...hi i have downloaded miRNA-seq RPKM-log data from TCGA portal. If i want to find the differentially expressed miRNA , can i used directly RPKM data or do i need to change

edger

updated 8.3 years ago • lily

Hello, I have different fcs datafile from MoFlo Astrios, and I want to transform it into log. I read the data with "read.FCS" from "flowCore" package but I haven't yet find a way to transform my data. How can I do it ? Thank...Hello, I have different fcs datafile from MoFlo Astrios, and I want to transform it into log. I read the data with "read.FCS" from "flowCore" package but I haven't yet…

transform flow cytometry data

updated 9.0 years ago • cr

files (indeed, the entire site that hosts them) is not functioning: http://genomique.info/data/public/RiboProfiling/ctrl.bam and the parent site, http://genomique.info is just an Apache landing page

RiboProfiling

updated 16 months ago • max.ferretti

I have seen peer-reviewed publications where Deseq2 is used for differential abundance analyses of 16s rRNA data. I've recently been informed that

Microbiome 16s Deseq2 16srRNA

updated 3.7 years ago • Katelyn

for scheduled maintenance. Thank you, Dan Tenenbaum Program in Computational Biology Division of Public Health Sciences Fred Hutchinson Cancer Research Center [[alternative HTML version deleted]] </div

Cancer Cancer

updated 15.3 years ago • Dan Tenenbaum