Bioconductor Forum

Community, in my current microarray analysis, based on a methodology we have developed in my lab to identify "hub" genes from DE genes lists (which i acquired also from limma with various comparisons/TREAT etc), we resulted in...hub genes. Thus, I would like to implement the function __plotRLDF() __to further test and identify a small subset of these genes, that separate my cancer from …

limma microarray plotRLDF classification

updated 9.6 years ago • svlachavas

Dear Rsamtools developers, I am dealing with bam files containing alignments from very highly multiplexed sequencing libraries generated by targeting ~ 1000 different genomic regions by PCR. (This is different from labeling different samples with barcodes. Here, regions from a single genome are amplified in parallel using ~ 1000 pairs of gene-specific primers and sequenced together.) Some of th…

rsamtools read group bam

updated 11.0 years ago • Thomas Sandmann

https://imgur.com/a/cnvCL)Dear all, Since I am using DESeq2 version 1.18.1 I observe a weird behaviour with the significant genes. As you can see on the heatmap below, the top 50 most significant...tried to pre-filter the gene list with no success (filtering lowly expressed genes for a certain number of samples). I have 3 different groups with 3 samples each and the filtering I added is having a…

deseq2 outliers version

updated 7.8 years ago • aec

<div class="preformatted">Hi, I'm using R 2.5.0 on openSUSE 10.2 x86_64. I'm using some agilent CGH data and thought the DNA copy package could be of some use. I'm trying to create the copy number array object using the CNA function. Usage: CNA(genomdat, chrom, maploc, data.type=c("logratio","binary"), sampleid=NULL) I've...CGH data and thought the DNA copy package cou…

GO marray GO marray

updated 18.3 years ago • jhs1jjm@leeds.ac.uk

gt; -> filterVcfMuTect2 -> filterVcfBasic Execution halted __below is the sessionInfo__ R version 3.3.1 Patched (2016-08-12 r71089) Platform: x86\_64-pc-linux-gnu (64-bit) Running under: Red Hat Enterprise Linux Server

PureCN

updated 8.2 years ago • xiao.qiao.liu

mart <- biomaRt::useEnsembl(biomart = "ensembl", dataset = "hsapiens_gene_ensembl", version = 107) biomaRt::getBM(attributes = c("entrezgene_id"), mart = mart) ``` returns the following error: ``` Error in .processResults(postRes...entrezgene_description" "entrezgene_accession" "entrezgene_id" ``` It seems to affect only version 107. The same code for 106 and 108 works with …

biomaRt Ensembl

updated 3.2 years ago • Marek Gierlinski

lt;- replace(mat, mat[5580, 4], "NA") I don't get any errors. However when I go to see if the number at mat[5580, 4] was replaced with "NA" the old number is still there. I don't get any errors. >mat.r[5580, 4] [1] 838.1 Any hints on...how to do this? Thanks, MAB [[alternative HTML version deleted]] </div

GO GO

updated 13.2 years ago • Mark B

hi I want to analyze the TCGA data with the DESeq2 package. As you know there are three types of data in this database. This site (http://seqanswers.com/forums/showthread.php?t=42911) provides information on these three types of data. 1- raw counts: The (first) RSEM paper explains that the program calculates two values. One represent the (estimated) number of reads that aligned to a trans…

deseq2

updated 5.7 years ago • roohallah1435

are input in other simulation tool and for this simulation I need using these SAM files with same version annotation file in GTF format. My question is how to find exactly same version annotation file relate to chromFa.tar.gz...GTF file from [UCSC](https://genome.ucsc.edu/cgi-bin/hgTables) but it is not exactly same version annotation file relate to chromFa.tar.gz I appreciate …

alignment BWA Burrows-Wheeler Alignment Tool

updated 7.5 years ago • modarzi

Hi, If I run the minimal example in R 3.6.3 it saves the files as shown in the screenshot and I think the console message is fine for this example. ![success with R 3.6.3][1] ![saved images with R Version 3.6.3][2] Switching the R Version to e.g. 4.3.1 leads to an error for the ssl connection. ![error message for R 4.3.1][3] I think this comes from a change in the package for th…

pathview SSL curl

updated 2.4 years ago • Matthias

header = T, sep="\t') note: phenodata.txt is a text file with variables in columns and samples number and/or names in rows. The output file appears to have the correct number of cases (133) and variables (20) Then I create a file...justRMA (sampleNames=x, phenoData=pD1) The output file, a matrix, opened in excel has the correct number of CEL files listed in columns (133 cases) and the correct…

Genetics Genetics

updated 21.8 years ago • Joshi, Nina NIH/NCI

I was trying to get some data from published RNA-Sequencing data, but to my surprise, the data analyses often seemed awfully incorrect to me. I would take the following paper published in Cell Stem Cell for example: * Sun D, Luo M, Jeong M, Rodriguez B et al. Epigenomic profiling of young and aged HSCs reveals concerted changes during aging that reinforce self-renewal. Cell Stem Cell 2014 May …

FDR p-value DESeq RNA-Seq

updated 8.0 years ago • yjiangnan

found, the 'ProbeID' is the same as the Array_Address_ID. The 'ProbeID' column was used in the old versions of Illumina BeadChip arrays, and it was later replaced with 'PROBE_ID" in the newer versions of BeadChips. >> >&gt...the NEQC function in the LIMMA package. >>> >>> I know there are traditionally a number of Illumina identi…

Microarray Annotation Normalization Clustering probe limma Microarray Annotation probe

updated 12.5 years ago • Wei Shi

the "-m intersection-strict" , and everything worked fine. However I do not know which htseq-count version was used as it was done within a Galaxy environment where I do not know the version, but most likely it comes from 2012...sam file everything works fine. The program terminates with an error after processing a substantial number of line pairs (for different .sam files it is a different numb…

updated 12.7 years ago • Mates Fendrych

colors = colors, rowLabels = rowLabels, : ERROR: length of colors vector not compatible with number of objects in 'order'.</span> 3) signif(diag(cor(blockwiseMEs[, single2blockwise], singleBlockMEs)), 3) # Code chunk 8<span style

WGCNA block size subscript out of bounds

updated 8.1 years ago • yifangt

EntrezIdentifier("org.Mm.eg.db")) GeneSetCollection names: chr5q23, chr16q24 (2 total) unique identifiers: (0 total) types in collection: geneIdType: EntrezIdentifier (1 total) collectionType: BroadCollection (1 total...hgu95av2.db")) > GeneSetCollection > names: chr5q23, chr16q24 (2 total) > unique identifiers: 35089_at, 35090_g_at, ..., 35807_at (79 total…

Cancer affy Cancer affy

updated 17.6 years ago • Martin Morgan

warnings as shown below Code should be placed in three backticks as shown below ``` Bioconductor version 3.16 (BiocManager 1.30.19), R 4.2.1 (2022-06-23) Installing package(s) 'DESeq2' Warning: unable to access index for repository...Loading required package: GenomicRanges Error in value[[3L]](cond) : Package ‘GenomicRanges’ version 1.50.1 cannot be unloaded: Error in unloadNamespace(packag…

DESeq2 version3.16 installation bioconductor GenomicRange

updated 3.0 years ago • hong

overload induced cardiac hypertrophy) which is based on MGUAv1 chip. I used CEL files from GDS41 (version 1) and MGUAv2 CDF file (version 2). I get all the expression values whose total number of probesets is 12654 which corresponds...to the one provided by version 1 chip. But I am wondering if the directions of probesets were fixed since I used the CDF version 2. Would it be ok to combine

Microarray cdf Microarray cdf

updated 20.6 years ago • Ryosuke Kadoi

data to the Drosophila reference genome. 3. Count uniquely aligning Drosophila sequence tags and identify the sample containing the least number of tags.--> **When they say tags, do they mean the Total Number of Reads after bowtie2

sperm Drosophila_melanogaster ATACSeq Normalization SpikeIn

updated 14 months ago • Katerina

annotate) library(genefilter) library(MASS) library(tkWidgets) library(mva) Now in the latest version of R/Bioconductor, I get the following errors when I use my .Rprofile >Welcome to Bioconductor > Vignettes contain

reposTools reposTools

updated 22.6 years ago • Claire Wilson

I followed the vignettes and tutorials I could find online as best, but got unexpectedly low number of DE genes. In the experiment, there are 2 subjects (X90 and X92) and 2 paired samples from each (Tom=control and Venus=treated...the cut-off value of 20? Thank you in advance for any insight/suggestions! ```r sessionInfo( ) R version 4.2.0 (2022-04-22) Platform: x86_64-pc-linux-gnu (64-bit) Run…

DESeq2

updated 3.2 years ago • mhalache

with __dba__ command: cannot allocate vector of size 2GB. I\`m running the most recent DiffBind version, 64-bit version of R on a computer with 8GB RAM. I reduced the number of samples from 6 to 4, but still get the same error only

R diffbind

updated 8.3 years ago • ekgush

Hi, I am trying to create a new package to submit to Bioconductor. I am trying to build the package using r-devel (version 4.4). For this I am using the docker image rocker/r-devel. My package vignette uses rtracklayer. When I try to install it...to create a new package to submit to Bioconductor. I am trying to build the package using r-devel (version 4.4). For this I am using the docker image…

newpackage rtracklayer

updated 22 months ago • Lucille

or criteria used to call gain, amplification, loss, and deletions? I know some might use arbitrary numbers as thresholds but I am curious about whether there is a better way to take into account case by case. In case, all my data...could be the best way to infer the threshold values to call aberrations? Shall I take the mean copy number of all probes across all samples to use it as the backgrou…

aCGH Cancer aCGH aCGH Cancer aCGH

updated 17.5 years ago • affy snp

<div class="preformatted">Dear List: Happy New Year! I have a question regarding mapping the gene to a copy number variations. I have affy 250 nsp mapping arrays results. Now I try to map the result for each probe to a gene. then, I can perform correlation analysis between the copy number variation and gene expression level for candidate genes. I think I have an idea t…

Annotation probe affy Annotation probe affy

updated 14.0 years ago • Xiaokuan Wei

Hi, I have two conditions (A, B) and two levels for each condition (Positive, Negative). Each group has ~4-5 biological replicates (Condition + Positive/ Negative). Based on exploratory analyses, I identified three outliers (A1Positive, B1Negative, A2Negative) which were removed from the downstream DESEQ2 analyses. I...has ~4-5 biological replicates (Condition + Positive/ Negative). Based on e…

Outlier

updated 2.8 years ago • sanchita.bhattacharya

My libraries contain on average ~7mln paired reads, and so round 500k reads map to cDNA. Is this number of reads enough? In the literature I found a following statement "Similarly, even with only 25,000-30,000 non-rRNA fragments...per sample we were able to identify 184 annotated genes in EDL933 whose abundance differed more than 2-fold between late exponential and early stationary

RNASeq Salmon DESeq2

updated 4.6 years ago • Mikołaj

<div class="preformatted">I am in the process of performing a meta-analysis on multiple MA studies run on several platforms and several species. Although I realize there are probably other ways to approach the data, my collaborators have chosen to use Cohen's D-statistic to summarize their data. I would like to use GSEA to look for over-represented groups or pathways in the data, but what …

PROcess PROcess

updated 18.8 years ago • Mark W Kimpel

<div class="preformatted">Hi, Please imagine the following situation: For two sample sets (set1, set2) the most differentially expressed genes are identified by limma. The p.value correction would be "holm". Afterwards a heatmap is printed for these genes. The procedure would...following situation: For two sample sets (set1, set2) the most differentially expressed genes are identified by…

Clustering limma Clustering limma

updated 19.1 years ago • Benjamin Otto

has been conducting a large scale analysis using TCGA data. I'm using the expression results to identify DE genes following the DESeq2 vignette along with lfcShrink (apeglm). I apply the analysis between healthy and diseased...of said results and the amount of bias introduced by such a big difference in the sample numbers representing each condition. Should I do something differently in the …

deseq2 cancer

updated 6.1 years ago • thanos5541

sample (pooled cDNA from a group of healthy control horses). When I use topTable to try to identify which genes are differentially expressed, the number with an adjusted P value < 0.05 is quite long (several hundred

Microarray Microarray

updated 19.1 years ago • Noah Cohen

network construction and module detection. There are 18 modules present in my network but could not identify the module colors. Can it be possible to get the different colors assigned to each module? I think the knowledge of...gmail.com amit.subudhi@pilani.bits-pilani.ac.in Mob No- 919983525845 [[alternative HTML version deleted]] </div

Network Network

updated 11.7 years ago • amit kumar subudhi

Can I do an equivalent job with Bio-strings yielding me such distance information, and can I also identify all the SNPs in an alignment with these large sequences i.e. the segregating sites? If so how? Many Thanks, Ben. [[alternative...HTML version deleted]] </div

Alignment Alignment

updated 12.2 years ago • Benjamin Ward ENV

beadchip. Is illuminaMousev2.db (GW6 v2) appropriate? At first I thought illuminatMouse GW6 format version 1 (illuminaMousev1.db) would include Mouse Ref-8 v1.1 probe annotation, but the identifiers (GI_xxxx) are different

Cancer Cancer

updated 14.5 years ago • Chao-Jen Wong

I'm using flowClust to identify cell subsets in flow data. I use the untreated samples to obtain a prior, which works well. However, w<span style="line...when using a prior. Labels are initialized from the prior.<br/> Using the parallel (multicore) version of flowClust with 4 cores"</code> I've tried setting different values for randomStart but it didn't help. It's not a problem

flowclust

updated 10.9 years ago • pavitrarc

the annotate package should help, but what I get from the function annotation is the GEO platform identifier: > library(GEOquery) > library(annotation) > data <- GEOquery(GEO='GSE13639') > annotation(data) [1] "GPL570" I'd like...package to install. Help will be much appreciated. Yours, Joern [[alternative HTML version deleted]] </div

Annotation annotate GEOquery Annotation annotate GEOquery

updated 15.8 years ago • Joern Grame

div class="preformatted">Hi, I am using RNA-seq data to identify the genes that are differentially expressed. I have two groups (eg., F0 and P6) with two replicates (a and b) for each group...of Plant and Soil Science email- sridhara@udel.edu Ph: 832-566-0011 [[alternative HTML version deleted]] </div

updated 14.8 years ago • Sridhara Gupta Kunjeti

library I believe my .geno and my .env files are formatted correctly, and I am using an updated R version. I also tried to install again the trio library, but apparently none of this helped. This is the command I am using, with...1 d = 1 *" [1] "********************************" Summary of the options: -n (number of individuals) 206 -L (number of loci) …

lfmm LEA

updated 4.6 years ago • valentinarov

following way:  <span style="background-color:white">(genome\_count(Set)\*10^9)/(window\_size\*number\_regions(Set))</span> I am assuming that genome\_count(Set) is referring to  "number of reads detected in each bin" and...that window\_size it the bin size. However, I am a bit unsure what number\_regions(Set) refers to? Is that the number of windows generated for …

MEDIPS

updated 10.8 years ago • malbert1

<div class="preformatted">Dear Manhong, I would just like to note here my own experience installing v12 on R 2.9.1 on MacosX. Using the R package installer I selected "Other Repository" and used the URL: http://brainarray.mbni.med.umich.edu/bioc/ Next I installed several custom CDF files in binary format and got the following error for every cdf I tried: Error in function (package, help, p…

cdf cdf

updated 16.4 years ago • Yair Benita

Hi there, I want to ask a question about number of interaction terms in a multiple linear regression model. I have a dataset with various predictors, including sample_group

limma linear regression model interaction terms

updated 5.8 years ago • yuabrahamliu

any function/parameter settings in R/BioC which adjusts the Heatmap image based on sample size and number of genes which needs to be plotted on image. The problem is when I generate Heatmap with : bitmap(file = Hfile, type = "png16m

updated 15.0 years ago • SAURIN

<div class="preformatted">Hi Hua, I hope that the dev version 1.3.10 now contains the feature both you and Khademul requested. I have added an option output =c("nearestStart", "overlapping", "both") to annotatePeakInBatch. Default will be "nearestStart" which is compatible to the old version. The option "overlapping" will output the overlapping features. The option "both" will output the …

PROcess PROcess

updated 15.8 years ago • Julie Zhu

and BSgenome.Hsapiens.UCSC.hg38 through bioconductor on my desktop (Windows) My current R version is 4.2.2.and bioconductor is 3.16 My command is this one: ```r if (!require("BiocManager", quietly = TRUE)) install.packages...gt; Warning message: package ‘BSgenome.Hsapiens.USCS.hg19’ is not > available for Bioconductor version '3.16' > > A version of this pa…

BSgenome.Hsapiens.UCSC.hg38.dbSNP151.major

updated 2.8 years ago • aubin

are not available, and `` sessionInfo() `` indicates that the installed version of graphite is 1.12.0, __not__ 1.14.0 (the most recent version, according to the above link). How do I update...my version of graphite and gain access to these functions? Thanks very much! <pre> > library(graphite) Loading required package...The following object is m…

graphite bioclite

updated 10.5 years ago • mhlinder

type the name of the targets file in the box. The same program worked fine with an earlier version of the same operating system last year and works fine on my Mac and Windows 2000 server. I would appreciate any suggestions...voice) friedman@cancercenter.columbia.edu http://cancercenter.columbia.edu/~friedman/ "Complex numbers! Ha! Ha! There is nothing weirder than imaginary numbers. Arc…

Cancer affylmGUI Cancer affylmGUI

updated 13.0 years ago • Richard Friedman

Hotbot C U S T O M E R Care Number ♻️ 86√88√20√26√65 💍 09832330695 Call Now All REfound 08688202665 Call Now All refound ComhdhdgHotbot C U S T O M E R Care Number...Call Now All REfound 08688202665 Call Now All refound ComhdhdgHotbot C U S T O M E R Care Number ♻️ 86√88√20√26√65 💍 09832330695 Call Now All REfound 08688202665 Call Now All refound Comhdhdg

hu6800probe

updated 2.6 years ago • kgu

the intermediate files are created but it doesn't finish the analysis. Here is the log:   R version 3.2.0 (2015-04-16) -- "Full of Ingredients" Copyright (C) 2015 The R Foundation for Statistical Computing Platform: x86\_64...and list types > library(derfinder) Find out what's changed in derfinder with news(Version == "1.2.0", package = "derfinder") > li…

derfinder software error rnaseq

updated 10.5 years ago • drramki.chop

<div class="preformatted"> hi all, the data set i have consists of x which is a matrix of 39 cancer patients [rows] and 2000 gene names [colmns]. each cell is the value of the gene for a particular patient. there are two types of cancer people representedas factor y. here is the code: library(e1071) #load database db <- read.csv(file="databases\\colon-cancer\\colon- cancer.cs…

Cancer Cancer

updated 12.5 years ago • Guest User

Hi all, I am using edgeR to identify genes differentially expressed in my experiment. I have cells which were grown in 4 different cell media and I would...Hi all, I am using edgeR to identify genes differentially expressed in my experiment. I have cells which were grown in 4 different cell media and I would like to perform an ANOVA to identify DE genes comparing all media vs all (e.g. media1 v…

edger error

updated 6.7 years ago • lucap

news group. This is the code I finally used: The summarised data is from ArrayExpress (accession number E-GEOD-22098). There is no bead-level data available. Each array is in a separate file, and the first 5 lines of the first...gt;>> TB1 > >>>>>> Error in object$genes[i, , drop = FALSE] : incorrect number of > dimensions &am…

Normalization probe safe ArrayExpress Normalization probe safe ArrayExpress

updated 14.7 years ago • Gavin Koh

library("org.Mm.eg.db") b<- addGeneIDs(annotatedPeak,"org.Mm.eg.db",c("symbol")) Error: No entrez identifier can be mapped by input data based on the feature_id_type. Please consider to use correct feature_id_type, orgAnn...or annotatedPeak * Thanks, Paolo > traceback() 2: stop("No entrez identifier can be mapped by input data based on the feature_id_type.\nPlease consider to use…

miRNA GO BSgenome BSgenome ChIPpeakAnno miRNA GO BSgenome BSgenome ChIPpeakAnno

updated 13.4 years ago • Paolo Kunderfranco

hg19 dbSNP, GRCh38, VCF</pre> <pre> > sessionInfo() R version 3.2.3 (2015-12-10) Platform: x86_64-pc-linux-gnu (64-bit) Running under: Ubuntu 14.04.4 LTS locale: [1] LC_CTYPE=ko_KR.UTF

annotation software error vcf annotationhub

updated 9.7 years ago • sskimb

Normalizing Calculating Expression Warning message: package âAnnotationDbiâ was built under R version 2.14.2 > c=paste(pd$treatment,pd$n,sep="") > f=factor(c) > design=model.matrix(~0+f) > colnames(design)=levels(f) > fit=lmFit...Loading required package: DBI Warning messages: 1: package âRSQLiteâ was built under R version 2.14.2 2: package âDBIâ …

convert convert

updated 13.7 years ago • michelle_low

MSGFplus and rTANDEM are both deprecated in Bioconductor version '3.16'. Are there any alternatives to perform peptide identification with spectral libraries

peptide peptideidentification rTANDEM MSGFplus Alternatives

updated 2.9 years ago • vaddanki

of covariates limma returns very few DEGs (7-32). From a biological standpoint, we expect a large number of DEGs for these comparisons. Below is the table of different versions of covariates and results of limma : Input Covariates

limma lmfit R DifferentialExpression

updated 3.6 years ago • Dimitris

seacr 2 seacr 3 seacr 4 seacr 5 seacr 6 seacr I would like to identify peaks that are different and similar between samples of the same group and also identify differences between groups...in how to do that would be great, I am kind of new in bioinfo. Thank you! sessionInfo( ) R version 4.1.0 (2021-05-18) Platform: x86_64-w64-mingw32/x64 (64-bit) Runnin…

DiffBind

updated 4.4 years ago • Danielle

<div class="preformatted">I quite like the idea of the positive border elements plots in affyQCReport. However, I have a few suggestions for improvements and would like to know what people think, and also how to go about achieving it. 1) I think the boxplots should use log2 intensities rather than raw intensities. 2) The way that +ve/-ve border elements are identified in the code essential…

GO probe GO probe

updated 17.5 years ago • Nathan.Watson-Haigh@csiro.au

dear All, was there any change to the biomart web service recently? Today I stumbled over the following problem when I wanted to list all available marts: <pre> > library(biomaRt) > listMarts() Space required after the Public Identifier SystemLiteral " or ' expected SYSTEM or PUBLIC, the URI is missing Opening and ending tag mismatch: hr line 7 and body Opening and en…

biomart bug

updated 9.7 years ago • Johannes Rainer

span, : NA/NaN/Inf in foreign function call (arg 1) Timing stopped at: 12.34 2.11 14.5 The number of NAs and weights in the offending array are; > sum(is.na(tmp$M)) [1] 717 > sum(is.na(tmp$A)) [1] 717 > table(tmp$weights) 0 1 8362...release of limma. A colleague independently tested normalizing the one offending microarray slide I identified causing the sa…

Normalization limma Normalization limma

updated 13.3 years ago • Gordon Smyth