Bioconductor Forum

where we have collected protein data from over 100 patients samples. This data is normalized and log transformed to achieve a uniform distribution. The goal is to cluster samples based upon their similarities, I am using

clustering hierarchical clustering

updated 8.4 years ago • hrishi27n

get the error below data <- normOffsets(data, type="loess", se.out=TRUE) Error in loessFit (log (mat [, x] + cont.cor.scaled [x]), ab, …) : unused argument (type = “loess” ) I tried running it on the initial data object and get the same error

diffhic csaw

updated 6.5 years ago • shopnil99

seq data. First, I have transformed my data using __VOOM__ transformation and then i would use the__ log-cpm__ values of the __E__ component of EList output object.The inverse variance weights, after voom, is a numeric matrix

rnaseq glmnet limma voom deseq2

updated 8.9 years ago • panagiotis.mokos

file? 1. Use PureCN's readCurationFile to read the .rds file into object RDS, then retrieve the log ratios of the marks in RDS$input$log.ratio 2. Compute the adjusted copy ratio of each mark by taking 2^log.ratio, then applying

PureCN

updated 7.3 years ago • twtoal

<div class="preformatted">Hello Everyone i used the function paCalls in package oligo to calculated detection pvalue for human gene 1.0 ST array at probeset level but fail with the error message: "error in log(paCalls(x,method="DABG",verbose=FALSE)) mathematical function used non-numeric parameter".( message was translated from Chinese...pvalue for human gene 1.0 ST array at…

oligo oligo

updated 14.3 years ago • marco

then taking the log2) If you want log2 CPM for each individual sample, please use cpm(y, log=TRUE) rather than log2(cpm(y)) > as wrong for plotting this certain result as it might not be a very > correct way in dealing...with the count data, or are it still log 2 cpm > values, but simply calculated in an other fashion and maybe with a > somewhat different in…

edgeR edgeR

updated 12.0 years ago • Gordon Smyth

This is the first time I have analyzed raw Illumina idat files and I have used neither Immuminaio nor lumi before. The problem I'll describe is not necessarily related to Illuminiao - it may be a problem with my idat files themselves

illuminaio idat beadarray

updated 10.4 years ago • willj

but then I didn't succed to do the conversion of my identifiers with "ids2indices" function? nor later the gene set testing? Please, find below my code, I'm new to Limma what am I doing wrong

limma agilent microarrays gene set testing annotation

updated 9.0 years ago • Bouzid.a

analysis. Here, I am not interested in contrasting groups (I don't have treated vs. untreated, nor tumours vs. normals, I just have a bunch of tumours). I only want to find a value for the expression level of the two genes I am

deseq2 tcga

updated 8.2 years ago • robles.daniela

character(0) ``` I'm truly lost here. I'm not even sure how data is stored in the gsets list nor even if the genes names are in that list for that matter. I'm sure I'm missing something very basic here but can't see what. Could

org.Rn.eg.db annotation go

updated 5.9 years ago • jose.wo

Hi, I am trying to perform quality assessment for bulk rna-seq data that I analyzed via DESeq2. I would like to try clustering samples on a heatmap showing genes that were variably expressed. I saw on the deseq vignette that it is possible to generate a heatmap of 20 genes with the highest mean expression using the following code: ```r library("pheatmap") select <- order(rowMeans(count…

DESeq2

updated 3.0 years ago • Josiah

in sacurine.oplsda[["subset"]] : this S4 class is not subsettable sessionInfo( ) R version 4.2.0 (2022-04-22) Platform: x86_64-pc-linux-gnu (64-bit) Running under: Ubuntu 20.04.3 LTS Matrix products: default BLAS: /usr/lib/x86_64

Metabolomics ropls

updated 3.2 years ago • ansari.maya022

GSE146963/GSE146963_RAW.tar', reason 'Permission denied' sessionInfo( ) R version 4.2.0 (2022-04-22 ucrt) Platform: x86_64-w64-mingw32/x64 (64-bit) Running under: Windows 10 x64 (build 22000) Matrix products: default locale

GEOquery

updated 3.4 years ago • Durga

la URL 'http://starbuck1.s3.amazonaws.com/sradb/GEOmetadb.sqlite.gz' sessionInfo( ) R version 4.2.0 (2022-04-22) Platform: x86_64-apple-darwin17.0 (64-bit) Running under: macOS Big Sur/Monterey 10.16 Matrix products: default BLAS

SRAdb GEOmetadb

updated 3.4 years ago • jfertaj

some help, thanks in advance. Detailed Session Info: ```r sessionInfo( ) R version 4.2.0 (2022-04-22) Platform: aarch64-apple-darwin20 (64-bit) Running under: macOS Big Sur 11.6 Matrix products: default LAPACK: /Library

genefilter

updated 3.5 years ago • Francis

CRAN: https://cran.rstudio.com/ Bioconductor version 3.15 (BiocManager 1.30.18), R 4.2.1 (2022-06-23 ucrt) Installation paths not writeable, unable to update packages path: C:/Program Files/R/R-4.2.1/library packages

GenVisR GenVis

updated 3.5 years ago • abhisikta

GO:0006463" "GO:0016082" "GO:0051016" "GO:0070897" ![results][1] sessionInfo( ) R version 4.2.0 (2022-04-22) Platform: x86_64-pc-linux-gnu (64-bit) Running under: CentOS Linux 7 (Core) attached base packages: [1] tools grid parallel

GO.db geneontology GOslim

updated 2.1 years ago • amanda

please also include the results of running the following in an R session R version 4.2.2 Patched (2022-11-10 r83330) Platform: x86_64-pc-linux-gnu (64-bit) Running under: Ubuntu 22.04.1 LTS Matrix products: default BLAS: /usr/lib

InteractionSet BuildReport

updated 3.0 years ago • martin.grigorov

div class="preformatted">Is anyone aware of a public resource (other than pubmed) for cataloging the influence of genes on one another? Ideally, a it would be a list of coefficients

updated 22.9 years ago • Jeff Sorenson

in advance, Massimo -- Massimo Pinto Post Doctoral Research Fellow Enrico Fermi Centre and Italian Public Health Research Institute (ISS), Rome http://claimid.com/massimopinto </div

goProfiles goProfiles

updated 16.6 years ago • Massimo Pinto

the next BioC release. Cheers, H. -- Hervé Pagès Program in Computational Biology Division of Public Health Sciences Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N, M1-B514 P.O. Box 19024 Seattle, WA 98109

Cancer SNPlocs Cancer SNPlocs

updated 10.5 years ago • Hervé Pagès

BiocManager::install("rtracklayer") } library(rtracklayer) bw = 'http://genome-ftp.mbg.au.dk/public/THJ/Seq2PlotR/examples/tracks/HeLa_3pseq/siGFP_xPAP_in_batch1_plus.bw' rtracklayer::import.bw(bw) ``` Which gives...In seqinfo(ranges) : Invalid argument > >mustOpenFd: Can't open http://genome-ftp.mbg.au.dk/public/THJ/Seq2PlotR/examples/tracks/HeLa_3pseq/siGFP_xPAP_in…

import.bw rtracklayer Windows http

updated 4.2 years ago • sla

that change across the treatment relative to the 0h/Control. I want to find genes that have a large (+/-) log fold-change at either 12hrs or 24hrs and then come back to 0 in 36hrs and 48hrs. My thought was to perform a pair-wise comparison...treatments and the Control. I would then take the significant genes for 12hrs and 24hrs and plot the log fold-changes for the comparisons. I also used the `l…

deseq2 timecourse michael love multiple time points

updated 6.3 years ago • cp1015

mtime ctime /Users/charmyshah/GSE28829/GSE28829_RAW.tar 157736960 FALSE 644 2022-12-12 10:50:20 2022-12-12 10:50:20 atime uid gid uname grname /Users/charmyshah/GSE28829/GSE28829_RAW.tar 2022-12-12 10:50

cdf

updated 3.1 years ago • Charmy

Position of Bioinformatics scientist (Full-time/Permanent) for the analysis of multiomics data in oncology, at Evotec Toulouse (France) to be filled as soon as possible. https://www.evotec.com/en **General Summary :** For our site in Toulouse, France, we have an exciting opportunity for a dedicated and professional Bioinformatics Scientist - Full time and permanent to join our Research i…

bioinformatics omics R oncology France

updated 4.2 years ago • vincent.piras

Lecturers of the course: Robert Gentleman, Head of Program in Computational Biology, Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle (WA), USA. Wolfgang Huber, European Bioinformatics...England (UK). Rafael A. Irizarry, Department of Biostatistics, Johns Hopkins University, School of Public Health, Baltimore (MD), USA. The course is organized by S.M.Iacus an…

Microarray Proteomics Normalization Preprocessing Cancer Microarray Proteomics Cancer

updated 20.9 years ago • stefano iacus

developing a software management ecosystem that could be valuable for finding and linking software, publications and users in the research community. You may be also be aware of a related project, the Data Discovery Index, which...Discovery Index that would enable researchers to find, cite, and link software and analysis tools publications and researchers. To ensure that the opportunities, challe…

software NIH index News

updated 11.3 years ago • Sean Davis

Montreal, Quebec, Canada George Michailidis, University of Michigan, Ann Arbor, Michigan, U.S.A. Publication Date: June 2008 Number of Pages: 384 This text presents a unifying, thorough, and accessible introduction to the...sku=C6367) Robert Gentleman, Fred Hutchinson Cancer Research Center, Seattle, Washington, U.S.A. Publication Date: July 2008 Number of Pages: 328 This practical guide foc…

Proteomics Cancer Proteomics Cancer

updated 17.4 years ago • Thomas, Judy

including visualization and comparison of screening results, and contribute to efforts to generate public resources for high-throughput screening data (e.g. GenomeRNAi). The candidate should also contribute to efforts to...motivated, have a Ph.D. degree in bioinformatics, biology, biochemistry or related field and a publication record in international peer-reviewed journals. Excellent knowledge o…

rnai high-throughput screening workflows Job

updated 10.5 years ago • e.schmidt

Hello everybody I faced a problem in analysis of the data set "_GSE27274_" by _limma_ package. The parameter "_Coef_" which shows "_logFC_" calculated by _limma_ is different from the one I gained manually. I calculated log2 of treatment expression values average divided to control expression values average. I have not experienced this problem in analysis of other datasets. Is th…

limma logfoldchange

updated 9.6 years ago • moradzadeh_k921

Hello all, does anyone knows how we can overlay expression data { coloring with up and down genes } in pathways using R package or any other script. Especially the results from SPIA package , we get the kegg link like this ... http://www.genome.jp/dbget-bin/show_pathway?hsa05200+999+22798+3915+36 73+3675+6776+4233+2260+2263+7039+3082+5899+5337+5579+112399+2034+9063+ 1029+355+650+5743+596+718…

Pathways limma SPIA Pathways limma SPIA

updated 13.6 years ago • Amit Kumar Kashyap

hi, I am working with an expression matrix, I think I will use ratios for analysis of 2 conditions, does anyone know how to change values in a matrix. if I have 3 in log2 => 2^3=8 in decimal, how I do that in R for an entire vector or matrix? Thanks

updated 18.6 years ago • D.Enrique ESCOBAR ESPINOZA

Hello, I am attempting to use edgeR (3.12.1)'s glmTreat() function to identify genes that are significantly up-regulated by >2-fold in one group over another. My understanding from Sections 2.12 and 4.4.8 of the edgeR User's Guide is that the log2 fold changes for each gene will be tested against the absolute value of glmTreat()'s lfc parameter, which would output differentially expresse…

edger

updated 9.7 years ago • le2336

An embedded and charset-unspecified text was scrubbed... Name: not available Url: https://stat.ethz.ch/pipermail/bioconductor/attachments/20050719/ dcbb69cb/attachment.pl

updated 20.5 years ago • weinong han

counts(object), locfunc = locfunc, : every gene contains at least one zero, cannot compute log geometric means ``` The only fix I have been able to find is a adding a pseudo count. However, I just came across the sfType argument

Microbiome DESeq2 RNASeq

updated 15 months ago • Caroline

a WCGNA analysis (signed network) on microbiome 16S data. I have transformed counts to centeres log-ratio transformed data (CLR) to address the compositional characteristics of the data and have obtained a pretty decent

Network Transcriptomics MicrobiomeData RNASEQ WCGNA

updated 3.3 years ago • Julieta

RELEASE_3_15 ``` Then in a browser, I go to http:// <my server="">:8787, where I'm able to log in to Rstudio-server. This works when using the tags RELEASE_3_15, RELEASE_3_14, and older tags. However, this does NOT work

Bioconductor

updated 2.4 years ago • patrick.turko

after converting raw counts to cpm from data file using command <pre> lcpm<-cpm(y, log=T) head(lcpm)</pre> gives first row with unique numeric ID which denotes gene names from data file. How to export name of genes

edgeR lcpm bioconductor

updated 7.8 years ago • Björn

<div class="preformatted">Hi, I have normalised my two channel arrays with loess and the output file calles MA object (i named as MA.loess) was saved. When i gave the command names(MA.loess), i saw it has the following rows [1] "targets" "genes" "source" "printer" "M" "A" I was trying to transfer it to a text file to go on with differential analysis and clustering since one week, …

GO Clustering GO Clustering

updated 17.2 years ago • r.kandimalla

limited. Your account access will remain limited until this issue has been resolved please log in your account by clicking on the link below: My Account Activity Regards Alliance & Leicester- Online Banking Security

updated 16.9 years ago • Alliance & Leicester- Online Banking

<div class="preformatted">Gordon wrote: >This isn't an error in limma of course, rather you have tried to use a >function (write.table) on an inappropriate object. Do you want to output >the normalized log-ratios? If so, you might try >write.table(MA$M, file="your_file.txt",sep="\t") I've tried write.table(MA$M, file="your_file.txt",sep...a >function (…

limma limma

updated 22.1 years ago • utepandragon@tiscali.it

ranks is low it should be okay, but the number 73.72% looks unsettling to me. I obtained the log fold-change using DESeq2. Is there anything I could do to fix the problem

fgsea

updated 4.7 years ago • zli1

the signals span about four order of magnitude. Does this mean the expressions output by rma are log-tranformed? if so, which basis should be used to recover non-transformed signals? Thank you Martino --------------------------------------- Martino Barenco CoMPLEX

affy affy

updated 22.7 years ago • Martino Barenco

help on how to access the contents of the expression set?   <pre> exprs(eset) gives the log-expression values. </pre> How do we access the contents like cell type description? For Instance, while working with the series

normalization affy

updated 7.4 years ago • mahm

the moment to get the fold changes I am having to code it out manually. Currently I am getting the log(TPMs) for every gene in the pathway, calculating the mean, then calculating a second mean per group. Next I divide one group

limma

updated 8.0 years ago • chris86

in tmp[1, ] : incorrect number of dimensions and then a few warning messages: NaNs produced in log(x) I get the same if I try different normalisation techniques or mle instead of eb... I have installled both the hgu133aprobe

gcrma gcrma

updated 22.5 years ago • Crispin Miller

fraction of genes is not differently expressed, then the adjustment strategies are used to let the log-ratios have a median(mean) of 0. But in my case, every spot would have the same observed signal in the genomic channel while

Microarray Normalization Microarray Normalization

updated 19.2 years ago • yanju@liacs.nl

plot=TRUE) Elist <-v$E  My questions are: 1) expression profile in Elist has performed log(CPM) and been normalized for library size, right?; 2) Has the expression profile in Elist incorporated the precision weights

Voom $EList

updated 8.3 years ago • anpham

Hi all. I have an expression matrix that consists of log2-transformed RPKM counts. When I read this matrix in to a SingleCellExperiment object, how does Bioconductor know that I am working with RPKM counts? Is there a way to specify that my counts are log2(RPKM) counts, rather than raw reads? Further, does the ```calcAverage()``` function in ```scater``` treat raw reads differently than log-tr…

rpkm scater calcaverage R expression

updated 6.8 years ago • kushshah

I have early embryonic development time series (normal, mutant & treated) RNA-seq counts data from multiple studies which I am planning to use for clustering genes. I have to remove the study/batch effects for which I am using Combat-seq using study ID as batches. Then for normalization and transformation, I am using VST with blind=TRUE option. I see that mean expression of genes is no lo…

DESeq2 Transcriptomics RNASeq

updated 3.0 years ago • Jayesh Kumar

poison). I am assuming how the model work in the context of gene expression is to pre-calcuate the log-fold changes of genes between two groups and that will be used to fit negative bionomial and then perfrom a test whether...the logfold change is significant. Am I right? In a setting of time-course, how does the log-fold changes are calculated in the presence of Time and Time:Treatment inter…

DESeq2

updated 3.4 years ago • synat.keam

code from the documentation. plotDE <- function(res) plot(res$baseMean,res$log2FoldChange,log="x",pch=20,cex=.3,col=ifelse (res$padj < .1, "red","black")) This one doesn't work at all. plotDispEsts <- function(cds){ plot(rowMeans(counts...cds, normalized=TRUE)), fitInfo(cds)$perGeneDispEsts, pch = '.', log="xy") xg <- 10^seq(-.5,5,length.out=300) lines(xg,fitI…

Network edgeR DESeq Network edgeR DESeq

updated 13.7 years ago • Xin Davis

res$ProbeName,res$GeneName,res$Des cription,res$P.Value,res$adj.P.Val,res$logFC,exp(res$logFC*log(2))) and after I add to this dataframe the normalized log intensities and weights: lg=data.frame(Ebgnorm$genes$ProbeUID[isGene

Microarray Microarray

updated 15.8 years ago • Benoit

consist of around 400 samples (around 50 normal). I have run DESeq2 to calculate logfoldchange and log expression. I have the result. Then, I decided to do some clustering to get smaller size of the samples. From this clustering...img alt="" src="https://i.imgur.com/EUpuyCS.png" style="height:568px; width:674px"/> Then, from the log expression that I got from DESeq2 for both subset and all …

deseq2 rnaseq

updated 8.2 years ago • bharata1803

return difference and p-value as list(diff, pval) # Fisher Z-transform zf1 <- 0.5*log((1 + r1)/(1 - r1)) zf2 <- 0.5*log((1 + r2)/(1 - r2)) # difference dz <- (zf1 - zf2)/sqrt(1/(n1 - 3) + (1/(n2 - 3))) # p-value pv <- 2*(1 - pnorm(abs(dz))) return(list(diff=dz, pval=pv

updated 21.5 years ago • Christian.Stratowa@vie.boehringer-ingel…

types; and was wondering what the best practice would be here. Both data sets are normalised and log transformed [in the scRNA seq workflow using Seurat::NormalizeData(object, normalization.method = "LogNormalize", scale.factor...10000) and in the bulkRNA seq workflow (edgeR::cpm(y, normalized.lib.sizes = TRUE, log = TRUE after TMM normalisation) ], so I am assuming that it is possible to com…

seurat edgeR spearman correlation scRNAseq

updated 5.7 years ago • tobias-messmer

seems to be working: - `libsize.drop <- isOutlier(sce$total_counts, nmads=3, type="lower", log=TRUE)` - `feature.drop <- isOutlier(sce$total_features_by_counts, nmads=3, type="lower", log=TRUE)` - `spike.drop <- isOutlier(sce

scater scran singlecellexperiment normalize qc

updated 6.7 years ago • kushshah

Control (C). Correct? Third question: In the majority of the cases, the data are transformed into log in base 2. Then, in these cases, I have: (Log2 T / Log2 C). Correct? In this case, Fold Change would be equal to 2^(Log2 T / Log2 C). OK? Fourth...question: Exists some case where the ratio between the T and C are made before the Log transformation? For example: Log2(T/C). In the way that I m…

GO limma GO limma

updated 20.6 years ago • Marcelo Luiz de Laia

cancerSite, "\_Processed.rds")) stopCluster(cl); difftime(Sys.time(),t1) \# scrpt end The log file details Standardizing Data across genes Fitting L/S model and finding priors Finding nAdjusting the Data LoadiAdjusting...Data across genes Fitting L/S model and finding priors Finding nonparametric adjustments +++The log stop here

MethylMix Preprocess_DNAmethylation

updated 8.0 years ago • an17

<div class="preformatted">Dear Juliet, Gordon, I am also looking into using pre-computed camera statistics, both to speed up computation for a webservice and also to enable statistics, such as F-statistic to be used that are not currently supported by the limma/camera package (AFAIK). So I am trying to de-compose the limma/camera-function to be able to make use of pre-computed statistics. …

Microarray Proteomics limma Category CAMERA GSVA Microarray Proteomics limma Category

updated 12.3 years ago • Pekka Kohonen