Bioconductor Forum

GSVA) gsva_es <- gsva(y, geneSets, parallel.sz=2) sessionInfo( ) #R version 4.2.2 (2022-10-31) #GSVA_1.46.0

GSVA

updated 21 months ago • Alex

CRAN: https://cran.rstudio.com/ Bioconductor version 3.16 (BiocManager 1.30.17), R 4.2.0 (2022-04-22 ucrt) Installing package(s) 'DSS' Warning: 无法在貯藏處https://bioconductor.org/packages/3.16/data/annotation/bin/windows

methylationArrayAnalysis ChAMP DMP DSS

updated 3.7 years ago • 16301050225

I am trying to use GVIZ to visualize some sequencing data. GVIZ is giving an error when loading the hg38 genome. I tried upgrading R and the Gviz package but I still see the error. Does anyone have any suggestions? Thank you! ```r > library(GenomicRanges) > library(rtracklayer) > itrack <- IdeogramTrack(genome = "hg38", chromosome = "chr4") Error in value[[3L]](…

R Gviz

updated 3.7 years ago • RUser743

Program: Biostrings (version 2.62.0), a Bioconductor package # Rundate: Mon Feb 7 01:49:32 2022 ######################################## #======================================= # # Aligned_sequences: 2 # 1: P1 # 2: S1 # Matrix: NA # Gap_penalty: 14.0 # Extend_penalty: 4.0 # # Length: 24 # Identity: 11/24 (45.8%) # Similarity

Biostrings Alignment

updated 3.9 years ago • Charles Plessy

obtaining per-observation scaling factors for length normMat <- normMat/exp(rowMeans(log(normMat))) normCounts <- myCounts/normMat #computing effective library sizes from scaled counts eff.lib <- calcNormFactors...combining effective library sizes with the length factors, and calculating offsets for a log-link GLM normMat <- sweep(normMat, 2, eff.lib, "*") norm…

tximport edgeR Normalization

updated 21 months ago • Marianna

Hi- Trying to run the `rpkmByGroup` function from edgeR, I get the error below. rpkmByGroup(y, gene.length= rep(1000, nrow(y))) Error in cpmByGroup.default(y = y, group = group, dispersion = dispersion, : formal argument "dispersion" matched by multiple actual arguments I think it is because `rpkmByGroup.default` runs cpmByGroup with the dispersion argument specified twi…

edger rpkm

updated 6.6 years ago • dario.beraldi

__Johns Hopkins Bloomberg School of Public Health__ __Department of Biostatistics__ __Post-Doctoral Fellowship Opening__ __Positions to begin Spring...__Johns Hopkins Bloomberg School of Public Health__ __Department of Biostatistics__ __Post-Doctoral Fellowship Opening__ __Positions to begin Spring or...ovarian cancers (HGSOC) using bulk and single-cell RNA-sequencing data. This is high…

job single-cell data science cancer genomics Job

updated 7.0 years ago • Stephanie Hicks

They should detail your use of Bioconductor, and how it has supported your research efforts, listing publications, or grant submissions (even better funded grant applications to any source) that have relied on software available...Thank-you, Robert -- Robert Gentleman, PhD Program in Computational Biology Division of Public Health Sciences Fred Hutchinson Cancer Research Center 1100 Fairvi…

Cancer PROcess Cancer PROcess

updated 20.3 years ago • rgentleman

Hello, I have several batches of scRNA-seq data, which are biological replicates, and would like to use mnnCorrect() from the scran package to correct for batch effects. Each batch should have a quite a different cell type composition, which is why I would like to use the MNN method. From the help page it says that: "The input expression values should generally be log-transformed." This is fine…

scran mnncorrect

updated 7.9 years ago • Dave Tang

div class="preformatted">hello, i was following the discussion about "vsn on log" array data. does it apply also for the RMA-preprocessed affy data? since the expression values are log-scaled, is it incorrect

Normalization affy vsn Normalization affy vsn

updated 19.6 years ago • Dario Greco

other similar ones) can still be found in the marray package. It simply provides a version of the log function that does not throw warnings when called with non-positive arguments: log.na = function (x, ...) log(ifelse(x > 0, x, NA), ...) Best

vsn marray vsn marray

updated 21.2 years ago • Wolfgang Huber

Hi,  according to my script here below, why DESEq2 calculations and my own are not identical? What am I missing? Any halp will be most welcome, thanks. David dds<- makeExampleDESeqDataSet(n=100,m=18)  dds <- DESeq(dds, betaPrior = FALSE) resultsNames(dds) res <- results(dds) res\[1,2\] \# \[1\] -0.3811565 my.log2FoldChange <- log(r…

deseq2 log2fc

updated 9.2 years ago • David Rengel

compared to the samples in the normal group). The "low" expression means the (possibly transformed) log(cpm) has a z-score < -2, where the z-score is calculated using mean and standard deviation of the normal samples. In order to...After the gene filtering and TMM normalization, should I use voom() in limma package to transform log(cpm) to values that are normally distributed? &nbsp

gene filtering edger limma

updated 7.9 years ago • Frocha

DEPARTMENT/LOCATION [Department of Clinical Biochemistry](http://www.jobs.cam.ac.uk/job/?unit=u00220) SALARY £29,301-£38,183 REFERENCE RG11199 CLOSING DATE 2 April 2017 We are seeking to appoint a Postdoctoral Research Associate in Genomics to join our internationally recognised team led by Professor Sadaf Farooqi, Cambridge, UK and funded by the Wellcome Trust. Our aim is to under…

genetics job genomics postdoc obesity Job

updated 8.9 years ago • njc65

extdata", "compdata", "data", package="flowCore")) myTransform <- transform("FSC-H" = log, "SSC-H" = log) mat <- matrix(c(500, 400, 400, 600, 650, 650, 500, 600, 750, 750, 600, 500), nrow = 6) colnames(mat) <- c("FSC-H", "SSC-H") myGate <- polygonGate...log(mat)) %on% myTransform # Subset is happy: nrow(Subset(fcsSet[[1]], myGate)) # [1] 10 …

flowCore ggcyto

updated 8.9 years ago • jaera

<div class="preformatted"> Hi, I am new to data analysis using R and i tried Flowcore and Flowclust so far and is very pleased with features given. I am using FlowClust to autogate the data. Where i got stuck was that i do not know how to plot log graph i.e 1) drawing a scatter graph where either or both the axis are log converted as my flowframe data is linear and i want to plot log values…

graph flowCore graph flowCore

updated 12.0 years ago • Guest User

<div class="preformatted">Hi Elin, Thank you very much for the quick response and elaborate and clear explanation! Cor -----Original Message----- From: Elin [mailto:elin@ebi.ac.uk] Sent: Wed 9/17/2008 11:08 To: Cor Lieftink Cc: bioconductor at stat.math.ethz.ch Subject: Re: [BioC] Definition of the CellHTS2 normalizePlates parameter scale Hi Cor, I hope I can help you out here. Let me …

Normalization cellHTS2 Normalization cellHTS2

updated 17.3 years ago • c.lieftink@nki.nl

Hi everyone, first time poster. I have resorted to this because I can't seem to find substantive answers to my question (or don't exactly fit my question), nor can I find much about it in the literature. We have a study where we are interested in finding: 1. detecting genes that are differentially...because I can't seem to find substantive answers to my question (or don't exactly fit my qu…

RNASeqData DifferentialExpression DESeq2

updated 2.1 years ago • Peri

being able to redistribute the sequences, which is why they don't appear in the probe sequence files, nor on netaffx. Best, Jim -- James W. MacDonald, M.S. Biostatistician Affymetrix and cDNA Microarray Core University of Michigan

Microarray Cancer probe Microarray Cancer probe

updated 19.0 years ago • James W. MacDonald

and interpretation in the complex area of reverse engineering. c) Commitment to public and open APIs leverages the user community's capabilities to discover problems and to fix them. While distribution...by Kulp, because users would lack access to key elements of the interface. d) Commitment to public and open APIs sharply reduces effort required to support multiple platforms. When compiled l…

Microarray GO Cancer cdf Microarray GO Cancer cdf

updated 22.5 years ago • Vincent J. Carey, Jr.

Thereby theta is relative to the group mean.   The prior on theta is thought as a log-normal distribution theta = log-normal (m\_0j, r\_0j^2). The mean (m\_0j) and variance (r\_0j^2) can be estimated from the data. To do so...cgi/viewcontent.cgi?article=2613&context=etd>; alpha 2.19, beta 2.20). The distribution of log(theta) should be normal distributed wit…

DSS dmltest bayesian statistics methylation

updated 7.7 years ago • floriandeckert

I'd like to make them available for R Bioconductor users. Is there any guidelines to make them public? best Imad

BSGenome

updated 4.7 years ago • Imad

Hi all, I'm trying to run ORFik on a folder of .fastas. These fastas are outputted by an earlier python script, they're HTS contigs marked as viral in origin. Everything runs fine until I need to extract just the ORFs from the fastas. Following the manual, I ryn findORFsFasta. The for loop is just to find each file in turn. It finds the ORFs fine, and the BioStringSet generates fine, I can print …

ORFik Bioconductor GenomicRanges Biostrings BSgenome

updated 3.3 years ago • Mog

Hi everyone, I'm currently analyzing a public microarray dataset (https://www.ebi.ac.uk/arrayexpress/experiments/E-TABM-104/) I've managed to import the GenePix...Hi everyone, I'm currently analyzing a public microarray dataset (https://www.ebi.ac.uk/arrayexpress/experiments/E-TABM-104/) I've managed to import the GenePix files...that those layout information can be in a ".gal" file, …

limma microarray layout

updated 7.0 years ago • Guillaume Robert

by edgeR to say upregulated versus down regulated? I am little bit confused here. When I checked the log fold changes I couldn't come to a conclusion. When I counted the number of genes <0, the number is more than 97. Am I doing some...2. If I want to do some pathway analysis, I am wondering which value I have to use. When I use log fold change values, some genes are not identified as diff…

edgeR edgeR

updated 14.6 years ago • puvan001@umn.edu

nbsp; T, bCounts = T)</span></code> 1. Are the concentrations and read count columns reported in log RPKM, or, log raw read counts normalized by sample with smallest library size? 2. Are the concentrations and read counts reported

diffbind

updated 7.3 years ago • Shamaine

c(2,2),mar=c(2,3,2,3)) for (i in 1:4){ plotMD(tfit, coef =colnames(tfit)[i], xlab = "Average log-expression", ylab = "log-fold-change", main = colnames(tfit)[i] ,status=dt3[,i], hl.cex=c(0.7,0.7,0.7)) abline(h=0,lty=3,col="red") } ``` The contrast

limma plotMD

updated 5.8 years ago • chodar

you could start making changes and then see when what breaks. Also, why do you want to set log="x"? The data that you are supplying for the x-axis, log2FoldChange, are already on the log-scale, so that argument does not seem

updated 13.8 years ago • Melissa.Martin@lshtm.ac.uk

hand side must be named ‘value’.     The S3 consistency warning does not return a violating function, so I'm not sure what to investigate. I've commented out my Class and methods .R scripts,  and re-built and

cmd check warnings s3

updated 9.4 years ago • anthonycolombo60

0 [4028] chr2 [148267271, 148269771] - | -1.564551101 The values returned violate the condition. It won't work at all without na.omit. I can coerce the GRanges object to a data.frame, do the selection

updated 13.5 years ago • Michael Muratet

bam goes to bed format, so I need to know if there is any reason to believe that such an input would violate some assumptions made by csaw. Also if there a simpler workaround to look at insertion sites, I would gladly consider

csaw ATAC-seq Tn5 insertions

updated 5.2 years ago • alexandre.blais

based on the NB variance ~ expectation relationships?) function, rather than the direct log transformed counts.     I tried limma-voom in my new datasets, which has more than 500 samples with various factors...separations by those known factors.      I noticed that plotMDS uses the log transformed TMM normalized counts directly.&…

limma-voom deseq2 EdgeR

updated 7.2 years ago • Raymond

<div class="preformatted">Hi all, I have already obtained a data set from Illumina Beadchip-HT12 experience and I would like to analyse them in R with Beadarray package. I have files with the following extensions (.txt, .csv, .idat, .xml, .locs, .tiff) with a text file called Metrics. I guess that only two files are required (.txt and .tiff), right ? Now, I try to use the following script,…

beadarray beadarray

updated 16.5 years ago • Leo Nitsche

d <- dim(tmp(tmp[, "FLAG"] == 1,]) > d 208 2 #### BUT x <- validData(data.rma) x <- log(x)/log(2) mads <- apply(x, 1, mad) > sum(mads > 0.25) [1] 3641 I don't get the same numbers for MAD filtering. Can someone please tell

xps xps

updated 15.5 years ago • Larry Singh

issue now been fixed? e.g: exon.counts <- fitDispersionFunction(exon.counts) Error in if (sum(log(coefs/oldcoefs)^2) < 0.005) break : missing value where TRUE/FALSE needed In addition: Warning messages: 1: In glmgam.fit(mm...disps[good], start = coefs) : Too much damping - convergence tolerance not achievable 2: In log(coefs/oldcoefs) : NaNs produced I'm using R 3.0.1 x86_64-pc-…

updated 11.9 years ago • Odhams, Christopher

Affy's free ArrayAssist Lite program), values are much higher. I'm assuming there is some kind of a log function happening in the R version. Is there any way to turn the log function off? I've looked through the options but can

Microarray plier Microarray plier

updated 20.6 years ago • Tarun Nayar

which type of data the function "normaliseWithinArrays" want. And, if i must apply the function log, before or after normalisation. So i'm a little lost. (no log) (no background) (raw data) my data profile : dat$R dat$G 49 35 118 34 29 101.5

Normalization Normalization

updated 19.7 years ago • sysra

to some arbitrary number that wouldn't give me trouble. I decided to avoid a value between 0 and 1 (logs would be negative or zero) and chose 1.5. Just because. I then used the RG data, corrected that way, to continue. I normalised...genes show higher on the diagonal). The FDR values also appeared reasonable. Surprisingly (to me), nor removing background, even when I had some slides that didn't …

limma convert limma convert

updated 19.4 years ago • J.delasHeras@ed.ac.uk

I created an ArrayQualityMetrics report of a Large ExpressionSet. The problem is that when I move the mouse over the points of the PCA plot , the corresponding array’s metadata are not displayed in the table to the right of the plot, as they are supposed to be. Also, the data points are not responsive as they should be, when they are clicked. Nor do they correspond when the sample boxes are check…

arrayQualityMetrics

updated 4.1 years ago • michael.s

the minfi package with preprocessed data generated from GenomeStudio .txt output files? I am using publically available data from ArrayExpress and unfortunately do not have access to raw .idat files. Best, E

minfi

updated 2.8 years ago • alyena

fa 6177311541 181 Longwood Ave Boston MA 02115 USA stvjc@channing.harvard.edu -----BEGIN PGP PUBLIC KEY BLOCK----- Version: PGP 6.5.8 mQCNAzqIeGUAAAEEAMJXU941vIornTS52rl6z7eo+A7wwB0km/idLnkxzIhc1uLi Qtn19OyOfG6IDSucLrtmpvwagemAnQ9jL6TVDrmlrKnqsh...DhhtT4mEAHt0E8dNBVCj+lKr3W vYS5GqO9gY4CiT3JXFH9N19pSbUQFiNDqpmG6EbWng== =DQNF -----END PGP PUBLIC KEY BLOCK----- </div

updated 23.6 years ago • Vincent J. Carey, Jr.

value = character(0)) : replacement has 0 rows, data has 979 sessionInfo( ) R version 4.2.1 (2022-06-23) Platform: x86_64-apple-darwin17.0 (64-bit) Running under: macOS Monterey 12.1 Matrix products: default LAPACK: /Library

scCATCH

updated 3.3 years ago • Chris

cumulative distribution function of the normal distribution. Then I've computed the corresponding log-likelihood function. The computation of maximum log-likelihood is possible but difficult. That's why I propose to solve...vector of intensities (perfect match). Then I suggest to make the following substitutions in the log- likelihood function: mu ----> mean(intensities)…

updated 22.4 years ago • Antille,Nicolas,LAUSANNE,NRC-BAS

networks with national and international players which makes it a competent partner for the general public, science, medicine, politics, and economics. ##Your Key responsibilities * Phylogenetic and genomic analysis of publicly...and challenging position centrally located in the Rhine-Main area (Frankfurt) with good public transport connections (motorways/highways, airport, and fast commut…

rna-seq phylogenetics protein modelling single-cell sequencing Job

updated 5.4 years ago • liam.childs

in the input VCF file by adding the number of entries > 0.9 in column "prior.somatic"?  (A log message said that variants marked SOMATIC were found and their prior probability was set to 0.999). PureCN.R is not seeing...gt; 0.9. What filtering might PureCN be applying to my somatic variants?  I didn't see log file messages indicating that a bunch of them had been filter…

PureCN Somatic Mutations

updated 7.7 years ago • twtoal

Could anyone please help me how to run multipollutant association model as mentioned in the below publication; https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8949945/pdf/ijerph-19-03292.pdf Many thanks

statistics Regression r limma

updated 2.1 years ago • Jitendra

I have noticed that several groupings of BRCA samples can be retrieved with "colData", and I would like to know how these groupings were obtained (algorithms, publications, etc.) Integrated.Clusters.with.PAM50 ? Integrated.Clusters.no.exp. ? Integrated.Clusters.unsup.exp. ? Thanks...be retrieved with "colData", and I would like to know how these groupings were obtained (algorithms, public…

TCGAutils

updated 6.8 years ago • vittorio.fortino

How to remove outliers from proteomic dataset before log 2 transformation

Proteomics Proteome

updated 3.3 years ago • bansalheena10

contains mappings based on older data because the original resource was removed from the the public domain before the most recent update was produced. This package should now be considered deprecated and future versions...for many people. I'm not sure what the original reason for removing the database content form the public domain is, officially I found the following information: Plea to sup…

updated 14.0 years ago • Asta Laiho

I'm using the RRHO package to compare ranked gene sets. The associated publication mentions that "the highest intensity point on the [RRHO] map can be used to extract the most statistically significant

rrho

updated 6.3 years ago • gideon.e

existing packages (e.g. minfi) can be readily applied to get the methylation data. Not too many publications yet, but there seems to be a dataset in GEO... thanks

illumina methylationEPIC 450k

updated 9.9 years ago • Brian Smith

p = .01, rather than "5" to mean P = .00001. One can get this effect buy using R's plot option log = "y" if you avoid transforming the p values into -log10 p values first. The problem is that now the volcano appears upside down...up. One can't simply multiply the the p values by -1, either, since then R attempts to take the log of negative numbers (of course). The only solution I can think…

updated 16.7 years ago • Thomas Hampton

<div class="preformatted">Dear Folks, Here is an interesting Post Doc position (see also http://www.nature.com/naturejobs/science/jobs/95047-Post-Doc-Position- Applied-Statistics-And-Bioinformatics): The University for Applied Sciences (UfAS) Wildau (Berlin, Germany) and Philips Research offer a 2-year Post Doc position in the field of mathematics, statistics, statistical pattern recognit…

Sequencing Microarray Proteomics Pathways Network Cancer Sequencing Microarray Proteomics

updated 16.7 years ago • Paul Hammer

using calnormFactors() function, but using counts from all none-DE genes. The second one is taking log of all the none-DE counts, and then calculate the median of log(counts)[,i]-log(counts)[,1], where i is the index of each individual...each row in the count matrix). Then I used norm<-norm/exp(mean(log(norm))) to make sure that all factors multiple to one. After that, I replaced …

Normalization edgeR Normalization edgeR

updated 11.4 years ago • Zhan Tianyu

Pathview is an open source software package distributed under GNU General Public License version 3 (GPLv3). Details of GPLv3 is available at http://www.gnu.org/licenses/gpl-3.0.html. Particullary, users...are required to formally cite the original Pathview paper (not just mention it) in publications or products. For details, do citation("pathview") within R. The pat…

MAGeCKFlute

updated 6.2 years ago • pamelalee

counts(object), locfunc = locfunc, : every gene contains at least one zero, cannot compute log geometric means* And I see that after applying mm1 <- mm1[,-idx] My mm1 that initially was num [1:46 , 1:15] it becomes num [1:46 , 0] Can...understand what am I doing wrong? Thank you. Laia > sessionInfo() R version 4.2.1 (…

DESeq2 design 0substract nofullrank

updated 3.2 years ago • Laia

and `coef` are ignored for `type="ashr"` when `res` is provided (and for `ashr` neither `contrast` nor `coef` are required). There is also the error message `one of coef or contrast required if 'res' is missing`, which appears to imply

deseq2

updated 6.8 years ago • tdanhorn

sep=",") > >In my cvs file I get the name of genes, but I don t get the "F.p.value" >nor "lods" values. You've asked for the names of the genes with small values of F.p.value, and that's what you got. >I try: > >todos20050401.fit3

updated 20.7 years ago • Gordon Smyth

heatplot(readable_gene_names, foldChange=gene_list, showCategory=5) sessionInfo( ) R version 4.2.2 (2022-10-31) Platform: x86_64-apple-darwin17.0 (64-bit) Running under: macOS Monterey 12.6.2 ``` ![heatplot genes overlapping][1] [1]: /media

heatplot enrichplot

updated 3.0 years ago • Melanie

Bioconductor version 3.14 (BiocManager 1.30.19), R 4.1.3 (2022-03-10) Installing package(s) 'org.Hs.eg.db' installing the source package ‘org.Hs.eg.db’ trying URL 'https://bioconductor.org

OrgDb

updated 3.0 years ago • hswdl