Bioconductor Forum

Dear All, I am using IsoformSwitchAnalyzeR package to identify recurrent isoform switches in a set of 24 rectal tumor samples. The isoform and gene quantification has been done...rectal tumor samples, I was interested in all possible pairwise comparisons between these samples to identify recurrently occurring switches. I created the $condition column with only one label "CRC", and the program …

cancer Isoform limma IsoformSwitchAnalyzeR

updated 6.2 years ago • asmita

I am reading about a new package and I am interested in plotting logo of a protein sequence. The problem is that the author did not specify how one can convert the sequence to number https://www.bioconductor.org/packages/devel/bioc/vignettes/motifStack/inst/doc/motifStack_HTML.html#plot-an-amino...sequence. The problem is that the author did not specify how one can convert the sequence to…

motifStack

updated 6.7 years ago • Bioinformatics

<div class="preformatted">I have the 3UTR sequence and the description in separated variables. How can I generate a list with the two elements $seq and $desc as expected by writeFASTA ? Thank you, Maura. ________________________________ Da: bioconductor-bounces@stat.math.ethz.ch per conto di Alvaro Cuadros Inostroza Inviato: gio 16/07/2009 16.24 A: 'Bioconductor List' Oggetto: Re: [BioC…

Transcription miRNA Biostrings Transcription miRNA Biostrings

updated 16.4 years ago • mauede@alice.it

Hi, I am working with NanoString GeoMx-NGS RNA Expression Data. The expression data has undergone appropriate QC, filtering, and Q3 -Third Quartile normalization, then by transforming the Q3 normalized data to log2 normalized data values, I plan to identify differentially expressed genes with `duplicateCorrelation` to estimate the correlation within subjects or repeated...normalization, then by …

NanoStringNCTools limma ExpressionData RNASeq edgeR

updated 18 months ago • mohammedtoufiq91

I have read the data using lumiR methoda and normalized the data using lumi Methods. Now I need to identify the differentially expressed genes by comparing each of these groups with each other. I am using linear model fit...in limma package and topTable method to identify top N differentially expressed genes. 1. When I am adjusting the p value using "BH" method in the topTable method the

Microarray limma lumi Microarray limma lumi

updated 16.3 years ago • Md.Mamunur Rashid

experimental conditions (group1, group2 and group3). When I run DESeq2 with groups 1 and 2 only, its identify 3239 genes as DE (p-value < 0.05). Here is output with inspection of one transcript, Omu_14977_c0_g2_i4, that is absent...7.074097 0.4003181 17.67119 6.990643e-70 2.067762e-65 ``` But if we run DESeq with all 3 groups, number of DE genes will be 752 only, almost 4 times lower: ```…

DESeq2 RNASeq

updated 2.7 years ago • Ilya

DE test between 10 cells vs another 10 cells, I nearly can't find any DEs. After I increased the number of cells to do DE test ( including above 20 cells), I can get about hundreds of DEGs. So may I ask is there minimum number of

MAST scRNAseq differential expression

updated 6.3 years ago • Andrew_McDavid

<div class="preformatted"> I used getSegmentReadCountsFromBAM() to get a GRanges object from a list of tumor-normal bam files Then I used referencecn.mops(). Whenever I try to calculate integer copy numbers using calcIntegerCopyNumbers() I get an error. This error can be reproduced using the data provided by cn.mops so this...of tumor-normal bam files Then I used referencecn.mops(). Wheneve…

cn.mops cn.mops

updated 11.8 years ago • Guest User

algorithms so that i am able to tell which genes are differentially expressed due to changes in copy number. I did a pubmed search and found only 7 literature pieces all of which use in-house algorithms. I am yet to explore Gviz...r-project.org; r-help@r-project.org Subject: Re: [BioC] Overlay Gene Expression on SNP (copy number) data On Mon, Apr 23, 2012 at 6:33 AM, Ekta Jain <ekta_jain@jubi…

SNP Coverage Network Cancer TranscriptDb IRanges RCytoscape ggbio Gviz SNP Coverage

updated 13.6 years ago • Ekta Jain

How one can display the number of downloads of his/her packages similar to R CRAN on their homepage

DMCHMM Tutorial

updated 6.2 years ago • shokoohi

<div class="preformatted">Hello, I've been using Bioconductor to do the background correction and normalization of my data, but I want to use the probe values themselves instead of a summary value for my statistical analyses. I am able to export the matrix of pm values, but the first column lists the AffyID and probe number together (e.g., 100_g_at1, 100_g_at2, 100_g_at3, etc.). Is there a…

probe probe

updated 22.4 years ago • Jenny Drnevich

use DESeq2 for a series of simulations on a high-performance computing cluster, but the most recent version of R available is 4.0.3. This means I can only use Bioconductor 3.12, and when I go to install DESeq2 using ``` BiocManager...for 3.12 anymore. Specifically: ``` package "DEseq2" is not available for Bioconductor version '3.12' ``` Can anyone help me with advice on how to ins…

DESeq2 BiocVersion

updated 4.5 years ago • Daisy

student doing research in a laboratory. We have collected flow cytometry data but would now like to identify the number of monocytes labeled with HLA-DR using Bioconductor in R. How would I go about doing that?</span

HLA bioconductor bioinformatics

updated 8.4 years ago • justinyi10

of samples, each repeated 6 times, so a total of 24 samples > and about 48,000 rows. how should I identify my sampleType in my case? also > what does colnames(design) <- c('100:0', '95:5-100:0') do, which columns > exactly does it take...is below: > > ################################################### > > ### code chunk number 30: filtering…

Microarray lumi Microarray lumi

updated 13.7 years ago • Minyue Wang

of subnetworks that correspond to tighter functional units, each represented as a list of KO identifiers (K numbers). For example MODULE: M00307 Ribosome, eukaryotes is defined as following list of 79 KO identifiers: K02981...K02942+K02943 My question is, how can i retrieve for each module the corresponding list of KO identifiers or for the KO identifier the Module it belongs to? Thank you in Ad…

updated 15.6 years ago • Alla Bulashevska

<div class="preformatted">Dear all, I am working on a ChIP-Seq data set. I want to compare two groups having only one sample each group. (no replicates in both group) I generated count matrix which element is the number of reads within gene region for each data set. I applied edgeR and DESeq methods for this comparison. For this case, 1. edgeR...one sample each group. (no replicates in b…

edgeR DESeq edgeR DESeq

updated 14.4 years ago • Woo, Sangsoon

from the above link to see if there is any tool that can convert GO annotations to Enzyme Commission numbers automatically. I went through the file at http:/www.geneontology.org/mapping/ec2go I have a big file which contains...GO Annotations and my objective is to convert those GO Annotations to Enzyme Commission numbers for further analysis. I would like to check if KEGG.db will be able to do …

GO convert GO convert

updated 12.8 years ago • Guest User

<div class="preformatted">Hi, The crlmm package implements copy number estimation for Affymetrix SNP 6.0 platform. The genoCN package has functions for identification of copy number states for Illumina SNP array. I am wondering how I could adopt crlmm package or geneoCN package to estimate copy number for the old Affymetrix SNP platforms (100k and 500k) using CEL files as input. I also t…

SNP crlmm genoCN SNP crlmm genoCN

updated 15.2 years ago • Julie Zhu

biocLite("BiocUpgrade")     \#\# R version 2.15 or later Error: Bioconductor version 3.4 cannot be upgraded with R version 3.3.2 which version of bioconductor...will work with R version 3.3.2 i am also not able to use other packages (eg airway) of bioconductor with this version of R.&nbsp

version compatibility

updated 8.8 years ago • farahqureshi5

Hello I have R version 3.6.1 on Linux and this is pretty immoveable due to dependencies of other packages. I want to install DESeq2. I run...Hello I have R version 3.6.1 on Linux and this is pretty immoveable due to dependencies of other packages. I want to install DESeq2. I run this...and the reason foreign fails is because it equires R>4.0.0 I can't really upgrade my R v…

error DESeq2 Install

updated 4.7 years ago • Mick

in isolation. What has helped me is thinking of the original scientific problem. We have a large number of genes, belonging (roughly speaking) to three groups: differentially expressed, non-differentially expressed, and...not expressed at all. Typically, our task is to identify the first group. Now, neglecting to pre-filter is equivalent to conflating the second and third groups (or, equivalent…

Microarray Microarray

updated 17.4 years ago • Assaf Oron

of sequencing - In some papers, they mention a "standard score (z-score) of Deseq2 normalized read numbers", if I am right, deseq2 count, and then normalized the count according to sequencing of each replica in order to be able...could be a good numerical value for the comparison...but, how could I get it the normalized read numbers or the Z-score? Thanks Gonzalo

deseq2

updated 6.8 years ago • gonzalo23mj

div class="preformatted">Hi Thomas, I've started to add support for versions 67 and 73+. I assume you're still using version 67 and have the data cached. How are you calling the script right now? Do...Valerie Obenchain wrote: > Hi all, > > As of this release ensemblVEP will support multiple versions of the > script. This will start with version 73 and move forward…

Cancer MLInterfaces bridge ensemblVEP AnnotationHub Cancer MLInterfaces bridge ensemblVEP

updated 11.9 years ago • Valerie Obenchain

array. I am now looking for a way to access the probe names, that is the probe set name plus an identifier. I have understood that this would be what would be the atom number in the custom spesification file. My affybatch...AffyBatch object size of arrays=754x754 features (88845 kb) cdf=E_colia530222N (11378 affyids) number of samples=20 number of genes=11378 annotation=ecolia530222n > N…

probe probe

updated 18.8 years ago • Karin Lagesen

<div class="preformatted">Try limma or maanova. --Naomi At 11:44 AM 1/22/2008, greg lefebvre wrote: >Hi all, >I have received time series dataset which I could not control the >experimental design. > >And here it is. This is a 2 conditions time series (placebo/treatment) with >5 time points. >The main issue I encounter is that the number of…

TimeCourse limma timecourse maanova TimeCourse limma timecourse maanova

updated 17.9 years ago • Naomi Altman

I tried to adapt this to my goal of creating an annotation data package with the Unigene Identifiers. I made some very minor changes and used the file samclonegb2 which is just a small text file with the first column...being a list of IMAGE cloneIDs and the second column is a list of GenBank accesion numbers. I used the following lines and the sampclonegb2 seem to load properly and then finally I…

Annotation Organism PROcess Annotation Organism PROcess

updated 22.0 years ago • Law, Annie

<span style="line-height:1.6">Hi,</span> <span style="line-height:1.6">I'm using </span><span style="line-height:1.6">SomaticSignatures package and i would like to find the best number of signatures that i should use. I could not find </span><span style="line-height:1.6">assessNumberSignatures</span><span style="line-h…

SomaticSignatures

updated 10.4 years ago • Asma rabe

variable si.origin<-c(rep(1,6),rep(2,3),rep(3,12)) 1 1 1 1 1 1 2 2 2 3 3 3 3 3 3 3 3 3 3 3 3 #Identifying regulated genes RP.adv.out<-RPadvance(si,si.cl,si.origin,num.perm=100,na.rm=FALSE,gene .names =si.gnames...error :( as follows* *Error in RPadvanceV1(data, cl, origin, num.perm, logged, na.rm, gene.names, : * * Number of classes and/or origins should match the columns in…

affy affy

updated 13.1 years ago • sai nitin

div class="preformatted">I cannot figure out how to install a development version of Bioconductor ( biocLite() ) The current version is 2.4 and I need to try something out in version 2.5 I must be easy. I have...mail archive with no result and the homepage only have information about how to install the current version. br - Morten [[alternative HTML version deleted]] </div

updated 16.1 years ago • Morten Hansen

hi I am using LIMMA to identify DEGs. I got the top 5 DEGs. But i am not able to get the whole list of DEGs with proper id and genes.  Here i used the code...nbsp; write.table(topTable(fit, coef=1, adjust="fdr", sort.by="B", number=500), file="limma\_complete.xls", row.names=F, sep="\\t") &nbsp

limma

updated 9.0 years ago • mathavanbioinfo

October 10, 2007 11:58 AM ??: Serge Eifes Objet?: Re: [BioC] Limma: Normalization with large numbers ofdifferentially expressed genes Quoting Serge Eifes <serge.eifes at="" lbmcc.lu="">: > > Dear all, > > We have performed...time-points and the p-values for the > moderated F-statistic after MHC (FDR, BH). > > Numbers of significant probes w…

Normalization Cancer PROcess Normalization Cancer PROcess

updated 18.2 years ago • Serge Eifes

bioconductor at stat.math.ethz.ch Date: Mon, Mar 2, 2009 at 10:10 AM Subject: Heatmap hints and identifying differentially expressed genes > Hi Amy, > > you can set up every color you want with this command: > > mycolors

updated 16.8 years ago • Amy Johnson

chip annotation packages that we distribute. Up to the previous release we have always included IPI identifiers (as part of the table containing the PROSITE and PFAM IDs). Unfortunately, [IPI](https://www.ebi.ac.uk/IPI) is no longer

annotation proteomics uniprot.ws News

updated 10.2 years ago • James W. MacDonald

<div class="preformatted">Hello there, At the moment, I use findOverlappingPeaks function to identified the overlapping peaks between two dataset A and B, and use makeVennDiagram to show the overlapping. However, I have...div class="preformatted">Hello there, At the moment, I use findOverlappingPeaks function to identified the overlapping peaks between two dataset A and B, and use make…

updated 15.0 years ago • Binbin Liu

Hey Community,   If I upgrade DexSEQ versions, will all of the files generated using the older version still be usable with the newer version?  Think major version

upgrade new version backwards compatibility

updated 10.8 years ago • jrdemasi

getReadCountsFromBAM(BAMFiles, sampleNames=paste("Sample",1: 3),WL = 5000, mode="paired") Identified the following reference sequences:  chr7,chr20 Missing "refSeqName"! Selecting chr7 as reference sequence...could not find symbol "keepNA" in environment of the generic function > sessionInfo() R version 3.2.0 (2015-04-16) Platform: i386-w64-mingw32/i386 (32-bit)…

cn.mops cnv cnvtools

updated 10.4 years ago • bioconductor

Pay: $37/hour (graduate student or profession), $22/hour (undergraduate) * Hours Per week: 10 * Number of openings: 1 **Summary:** The Office of the Vice Provost for Advances in Learning at Harvard (VPAL) is seeking a qualified...data-analysis-for-genomics)*, with a total of seven courses. These are currently written for R version 3.6.3 and (for the second series) Bioconductor 3.10. The courses …

JobPosting

updated 4.2 years ago • Colin

Hello everyone, I am trying to increase the number of outliers identified and replaced in my use of DESeq2. I create my DESeq object and get the following result ``` ## Create...As I understand it, this means that 39 genes (i.e. rows from count_file[,c(2:43)]) were identified as having at least one count above the default cook's distance threshold--which in my case is 0.99*F(7,42-7) = 3…

deseq2 outliers cooks cooks distance

updated 5.3 years ago • donnenfieldjonah

<div class="preformatted"> Dear Gunter, I am wondering if there is a limit on the number of tumor-normal pairs that referencecn.mops() can handle because whenever I give it more than 2 pairs, I get an error saying...div class="preformatted"> Dear Gunter, I am wondering if there is a limit on the number of tumor-normal pairs that referencecn.mops() can handle because whenever I give it mo…

updated 11.8 years ago • Guest User

Error: With R version 3.5 or greater, install Bioconductor packages using BiocManager; see https://bioconductor.org/install

software error Tutorial

updated 6.3 years ago • naeemurself

<div class="preformatted">Dear Luo and list, I am successfully using GAGE and pathview for my analyses and I like the package a lot. So, thanks for developing it. I have some points on which I would appreciate some help and/or clarification. AVERAGE VALUE - The first time I run the analysis with GAGE, I used an identical setup parameters as the example prepared by you in the manual. I ha…

gage pathview gage pathview

updated 12.2 years ago • Christian De Santis

Hi, I need to use an old protocol that use GenomicRanges 1.28.3 with R 3.4.0. I have this R version and genomicRanges 1.30.3. Is there anyway to specify which version of the package we want to install please ? I read...this page : https://www.bioconductor.org/install/ (Legacy and Older R Versions) and I search on internet but I did not find how to specify the version of the package. …

"genomicranges" "R"

updated 5.8 years ago • celine.labbe

I've found another issue with rtracklyer, where if I run a query with range specified as a large number of small GRanges, it seems to only be getting results for the first 1000 ranges. Again, hopefully the code below will...lt;- "hg19" >> > >> > >> > #### make some sample ranges - a large number of small ranges: >> &…

Cancer Cancer

updated 12.3 years ago • Janet Young

trials and epidemiology. The basic scientists are integrated into an INSERM unit whose goal is to identify and validate new gene signatures and drug targets. We approach the problem at three levels: Identification, Preclinical...of data produced by multiple different technologies. The goal is to create tools that can be used to identify new oncogenes and tumour suppressor genes, and to identify g…

SNP Sequencing Genetics Cancer Breast SNP Sequencing Genetics Cancer Breast

updated 15.6 years ago • Audrey Kauffmann

p/9137703/](https://support.bioconductor.org/p/9137703/). I would like to be able to access specific versions of Biocoductor packages. Typically, it would be great to be able to query and install package versions within a single...file that contains all archived package versions (which makes it easy to find them without parsing HTML files). It is in https://cran.r-project.org/src/contrib/Meta/ E…

Bioconductor

updated 2.7 years ago • Gábor Csárdi

div class="preformatted">Dear group, Which package can get me the chromosome number and coordinates of that gene on the genome along with gene names. Is there any such package or function? Thanks in advance

updated 21.1 years ago • S Peri

It seems that the source url of the GenomeInfoDbData version 1.2.9 are not up to date, both from the bioconductor related page and also when trying to install from bioconda chanel...of conda/mamba. Do you have any suggestion until fix on what version could be use/ where to find a version that can be used directly in conda and compatible with R version 4.2 ? I need to install

GenomeInfoDbData

updated 2.1 years ago • remi.trimbour

I have analysed the data using three different versions of DESeq2  v.1.10, v.1.14 & v.1.16 values are varying even after using  lfcShrink and betaprior=TRUE...I have analysed the data using three different versions of DESeq2  v.1.10, v.1.14 & v.1.16 values are varying even after using  lfcShrink and betaprior=TRUE while...involves shrinkage and …

rnaseq r deseq2

updated 8.1 years ago • minie

Hi all, Hopefully this is the right mailinglist for my problem: I'm searching for an older version of the data-package org.Hs.eg.db. More exactly: a version of september 2010 I compared a programms output I got in R...with the output of GeneTrail (an online Tool). GeneTrail uses a database version from 2010-09-02. I'm getting different outputs and was wondering if I made a mistake in my program…

updated 11.6 years ago • Guest User

Dear All! I have align  a total stranded RNA using STAR and count the gene level using htseq count. All the sample on RNASeqQC have more then 60ML of total reads and more than 40 ML of uniq reads, When I import on DESeq2 object and I try to see the number of element I found this: <pre> colSums(assay(rld) colSums.assay.rld...1e.06 A 0.114 B …

deseq2 start

updated 10.3 years ago • aristotele_m

AA Kredit Loan CusTomer Care Helpline NuMbeR ☎️ 7008172090//9199748209callme helpline number any problem solve

lpNet

updated 2.6 years ago • Sonu

AA Kredit Loan CusTomer Care Helpline NuMbeR ☎️ 7008172090//9199748209callme helpline number any problem solve

hu6800probe

updated 2.6 years ago • Lil

AA Kredit Loan CusTomer Care Helpline NuMbeR ☎️ 7008172090//9199748209callme helpline number any problem solve

regutools

updated 2.6 years ago • ajit

AA Kredit Loan CusTomer Care Helpline NuMbeR ☎️ 7008172090//9199748209callme helpline number any problem solve

hu6800probe

updated 2.6 years ago • Chulu

the data is from Illumina HT-12 chip, the getchipInfo() returns "HumanWG6_V2_11223189_B" as chip version. Any information or suggestion regarding this issue will be really appreciated. regards, Mamun ################################################## Here is the LumiBatch...of data information: Data File Information: Illumina Inc. BeadStudio version 3.4.0 …

Microarray Normalization Cancer Breast lumi Microarray Normalization Cancer Breast lumi

updated 14.5 years ago • Md.Mamunur Rashid

the prior when looking at comparatively large data sets? Or is edgeR less smoothing in the latest version. thanks Simon. > > > On Wed, 9 May 2012, Gordon K Smyth wrote: > >> Hi Simon, >> >> edgeR does take into account the...plots of the estimated >> dispersions, and sometimes if there are obvious outliers we w…

RNASeq GO edgeR RNASeq GO edgeR

updated 12.4 years ago • Simon Melov

0      1      1  ….. .. ... when i tried finding the best number of signatures  based on RSS and explained variance plots, it was 5 ,when i normalized the counts by the total number...of events observed in each sample, i.e. dividing by the column sums, the best number of signatures became 10, Any idea??   Thank …

somaticsignatures

updated 10.3 years ago • Asma rabe

Dear Users, I recently updated R version from 3.2 to 3.3 for the purpose of some package requirements. It needs to update package GenomicRanges to higher...Dear Users, I recently updated R version from 3.2 to 3.3 for the purpose of some package requirements. It needs to update package GenomicRanges to higher version, the current version of GenomicRanges is 1.22.4. I used source("https://bio…

genomicranges

updated 8.9 years ago • jial2

Can I pre-set the number of clusters with scater? I'm comparing scRNAseq analysis tools, and the same dataset clustered into 8 by Seurat is clustered

scater scran scrnaseq clustering

updated 7.0 years ago • shbrief

AA Kredit Loan CusTomer Care Helpline NuMbeR ☎️ 7008172090//9199748209callme helpline number any problem solve ✨tc

lpNet

updated 2.6 years ago • Chulu