Bioconductor Forum

identities while the smaller data set contained half as many piRNA identities. Is there a minimum number of gene identities required in order to analyze differential expression in edgeR? Best, Eleanor [[alternative HTML...version deleted]] </div

updated 11.7 years ago • Eleanor Su

<div class="preformatted">Hi, I have replicate sample counts for 2 groups but one sample is 4x number of mapped reads Than the other samples. 528,428 625,889 498,569 2,328,333 I divided all the mapped transcript reads by 4...div class="preformatted">Hi, I have replicate sample counts for 2 groups but one sample is 4x number of mapped reads Than the other samples. 528,428 625,889 49…

edgeR edgeR

updated 14.2 years ago • Lana Schaffer

gene.map[,"ensembl_transcript_id"]) [1] 246 Surprisingly, I get fewer 3utr sequences than the input number of ensembl_transcript_id. > length(gene.seq[,"3utr"]) [1] 216 How come ? Thank you in advance, Maura tutti i telefonini TIM...alternative HTML version deleted]] </div

updated 16.4 years ago • mauede@alice.it

div class="preformatted">Dear all, Could you please tell me why there is large differnce in number of differntially expressed genes obtained from cufflinks and DESeq. I found nearly 3000 upregulated genes at FDR...length bias, a general problem in RNA seq data analysis? Regards Aniket [[alternative HTML version deleted]] </div

DESeq DESeq

updated 15.3 years ago • Aniket Vatsya

<div class="preformatted">Hi, I had two sets of genes (say gset1 and gset2) drawn from a universe of N genes. I use GO to determine the terms that are enriched in gene set (say, GOterms1 and GOterms2). Is there a way that I can check the significance of the number of overlapping terms in GOterms1 & GOterms2 (i.e. significance of intersection of GOterms1 & GOterms2)? I have…

GO GO

updated 11.8 years ago • Tim Smith

I should mention that my sample size is n = 160.  I am wondering if the problem with increased number of hidden variables comes from the fact that some of the slides only have one case, while other slides have three cases...sample size was n = 850.  Thank you for your help. Jonelle Villar, RN > sessionInfo() R version 3.4.4 (2018-03-15) Platform: x86\_64-w64-mingw32/…

combat sva

updated 7.7 years ago • jonellevillar

is installed the cdf package but don't know what to do with it. Many thanks for your help. Alex R version 2.5.0 (2007-04-23) i386-pc-mingw32 locale: LC_COLLATE=English_United Kingdom.1252;LC_CTYPE=English_United Kingdom.1252...Roslin Institute is a company limited by guarantee, registered in Scotland (registered number SC157100) and a Scottish Charity (registered number SC023592). Our register…

rae230a cdf affy gcrma matchprobes rae230a cdf affy gcrma matchprobes

updated 18.4 years ago • alex lam RI

9. How do I retrieve the affyIDs of those 3 and 9 genes? Many thanks, Alex > sessionInfo() R version 2.6.1 (2007-11-26) i386-pc-mingw32 locale: LC_COLLATE=English_United Kingdom.1252;LC_CTYPE=English_United Kingdom.1252...131 5274471 Roslin Institute is a company limited by guarantee, registered in Scotland (registered number SC157100) and a Scottish Charity (registered number SC023592…

GO rae230a GO rae230a

updated 17.8 years ago • alex lam RI

During the workflow all seems fine until I merge the forward and reverse dada objects. Then the number of retained reads drops drastically from ~2xx000 to 0-50. ### What I did - demultiplexed my Illumina HiSeq 16S (V4) raw paired

dada2 515F - 806Rd

updated 5.8 years ago • beginner87

use a combination of both padj and fold change ratio to define differentially expressed genes (DEGs) identified by DESeq2. Would it be valid to submit a manuscript where the DEGs are identified only with a padj threshold? Many

deseq2

updated 5.4 years ago • marija.buljan.2

I have a RNA seq data which I am trying to identify DEGs. Dataset contains Untreated - 2 replicates (time point 0hr) Treated - 4 replicates (2 replicates at 6hr and 2 replicates...I have a RNA seq data which I am trying to identify DEGs. Dataset contains Untreated - 2 replicates (time point 0hr) Treated - 4 replicates (2 replicates at 6hr and 2 replicates at 12 hr) I merged all the samples and tr…

LRT co-expression network deseq2 time course experiment network analysis

updated 7.8 years ago • aishu.jp

factors contributing to antipsychotic response and adverse drug reactions. Furthermore, we aim to identify genetic susceptibility factors contributing to schizophrenia and the related symptoms. A cohort of first-episode...of candidate genes. The exome analysis will include, among other things, the examination of copy number variation. Furthermore, the postdoctoral fellow will be responsible for i…

Sequencing Genetics Pharmacogenomics Sequencing Genetics Pharmacogenomics

updated 13.7 years ago • Warnich, Louise <lw@sun.ac.za>

I've successfully run csaw and identified windows with significantly different ChIP-seq enrichment across my experimental conditions. Instead of producing...outlined in the user manual, I would simply like to export the total (or ideally, mean per base) number of reads, scaled by the normalization factors, for each input sample so that I can represent the signal over differential...10000, param=p…

csaw edger chip-seq

updated 8.4 years ago • jms1223

dimensions > # lets output data for all comparisons and adjust lfc > tt.1<-topTable(fit.eb, number=Inf, p=0.05, adjust.method="none") > dim(tt.1) [1] 1482 8 > tt.2<-topTable(fit.eb, number=Inf, p=0.05, adjust.method="none", lfc...2) > dim(tt.2) [1] 1482 8 > tt.3<-topTable(fit.eb, number=Inf, p=0.05, adjust.method="none", lfc=10)…

limma limma

updated 13.9 years ago • Vladimir Zhurov

<div class="preformatted">Hi I'm currently running Bioconductor version 2.2.0 under Windows XP x64 with 16 Gb RAM and Virtual Memory upto 100 Gb. In trying to combine 67 Affy u133a and 67 Affy u133a_2 cel files I am able to form the initial affy batches using read.affybatch() but get a memory allocation error (below) when I try to combine them with the 'combineAffyBatch()' function Error…

affy affy

updated 19.6 years ago • Carleton Garrett

array. 6. Apply empirical Bayses statistics and use topTable to generate a list of differentially identified peptides for the red channel (IgG) and green channel (IgA) respectively. This is an example of the script I'm using...peptide array studies have removed false positives from the analysis. The false positives can be identified by incubating the array with just the secondary fluorescent ant…

limma limma

updated 15.6 years ago • K.Z.Nambiar@bsms.ac.uk

but >= 1.6.0 is required by 'annaffy' I want to get GOALLLOCUSID and I am trying to get new version of GO and I could not find it. > GOLocmap<-mget(names(myGOCC$intCounts),GOALLLOCUSID); Error in mget(names(myGOCC$intCounts

GO GO

updated 21.2 years ago • Saurin D. Jani

To the developers, I've been working on differential expression analysis of drought-tolerance in rice. I have 2 genotypes (tolerant and susceptible) and 2 conditions (drought and well-watered) with 4 replications each, essentially a 2x2 factorial experiment with 4 replications. One of my main objectives is to identify drought-responsive genes. I set-up the codes as follows: <pre> colDat…

deseq2 ANOVA design interaction term

updated 7.9 years ago • tarun2

for lazy loading Warning in fun(libname, pkgname) : mzR has been built against a different Rcpp version (1.0.7) than is installed on your system (1.0.8.3). This might lead to errors when loading mzR. If you encounter such issues...file, DLLpath = DLLpath, ...) : unable to load shared object '/Library/Frameworks/R.framework/Versions/4.1/Resources/library/pdftools/libs/pdftools.so': dlopen(…

mzR Bioconductor

updated 3.7 years ago • weiping.li93

INDEL, IDV, IMF, DP, VDB, RPB, MQB, BQB, MQSB, SGB, MQ0F, ICB, HOB, AC, AN, DP4, MQ info(header(vcf)): Number Type Description INDEL 0 Flag Indicates that the variant is an INDEL. IDV 1 Integer Maximum number of …

vcf variantannotation granges

updated 9.9 years ago • georgewwp

of indices for each probe probe.zoneID         vector of zone ID numbers for each probe bgCells                    number of background...cells for the GeneChip NumberZones  …

updated 15.8 years ago • Dr Gyorffy Balazs

min.n, offset = offset, method = method.bin, : # With 4514 genes and setting the parameter minimum number (min.n) of genes per bin to 500, there are only 5 bins. Using 5 bins here means that the minimum number of genes in each of the...5 bins is in fact 515. This number of bins and minimum number of genes per bin may not be sufficient for reliable estimation of a trend on the dispersions...y.f…

edgeR edgeR

updated 12.6 years ago • Natasha

including differential gene expression, ChIP analysis of DNA-bound proteins, SNP detection, copy number analysis and structural variation. You will also gain experience in experimental design and downstream analysis...techniques, such as identifying gene signatures and regulatory networks. You should have a first degree in a scientific or computational discipline

Sequencing Microarray Cancer Sequencing Microarray Cancer

updated 16.4 years ago • Mark Dunning

Bioconductor 2.5 1. Install R 2.10.0. Bioconductor 2.5 has been designed expressly for this version of R. 2. Follow the instructions here: http://bioconductor.org/docs/install Please visit http://bioconductor.org for...packages/2.5/bioc/html/CGHnormaliter.html 6. ChIPpeakAnno Batch annotation of the peaks identified from either ChIP-seq or ChIP-chip experiments http://bioconductor.org/packa…

Sequencing miRNA Microarray qPCR Annotation Network Bayesian Regression CGH stam Rintact

updated 16.2 years ago • Patrick Aboyoun

Hi, I am using R version 4.3.1, R studio version 2023.6.1.524, isoformSwitchAnalyzeR version 2.0.1. I imported Salmon dataset via Tximeta...in estimateDispersionsGeneEst(x, maxit = maxit, quiet = quiet, modelMatrix = modelMatrix, : the number of samples and the number of model coefficients are equal, i.e., there are no replicates to estimate the dispersion. use

salmon IsoformSwitchAnalyzeR tximport RNASeqData

updated 2.4 years ago • elva.gypsophila

the original design matrix includes the covariates. Error in contrasts.fit(fit, contrast.matrix) : Number of rows of contrast matrix must match number of coefficients In addition: Warning messages: 1: In rn != cn : longer object...1100 Bates, Room 8070 Houston, TX 77030 713-798-4634 fax: 713-798-7187 [[alternative HTML version deleted]] </div

updated 14.4 years ago • Belmont, John W

is: AffyBatch object size of arrays=712x712 features (221801 kb) cdf=ATH1-121501 (22810 affyids) number of samples=56 number of genes=22810 annotation=ath1121501 notes=Merge from two AffyBatches with notes: 1) Merge from...AffyBatches with notes: 1) Merge from two AffyBatches with notes: 1) , and 2) , and 2) , and 2) R version 2.0.1 gcrma versionl 1.1.3 I would really appreciate some feedback…

gcrma gcrma

updated 20.9 years ago • Dion Whitehead

dbSNP NOT FOUND Error in getBM(attributes[c(3:6, 16, 17, 28, 62), 1], filters = "ensembl_gene", : Number of columns in the query result doesn't equal number of attributes in query. This is probably an internal error, please...report. > sessionInfo() R version 2.8.1 (2008-12-22) i486-pc-linux-gnu locale: LC_CTYPE=en_US.UTF-8;LC_NUMERIC=C;LC_TIME=en_US.UTF-8;LC_COLLATE=en_US

biomaRt biomaRt

updated 16.8 years ago • Lakshmanan Iyer

c<-makeContrasts(group2-group1,levels=design) ** * topTable(fit2, coef=1, adjust="fdr", number=10) ID logFC AveExpr t P.Value adj.P.Val B 8516 253416_at *7.122005* 7.535481 26.57534 2.255100e-05 0.3000238 1.4319777...OR **c<-makeContrasts(group1-group2,levels=design) *topTable(fit3, coef=1, adjust="fdr", number=10) ID …

updated 15.6 years ago • varpal singh

div class="preformatted">Dear Adi and all members, I have been trying to analyze and identify unique genes and their association with signal pathways by using SPIA package. Here is the link of one of the pathways...works. Many many thanks and have a great holidays for all Jing [[alternative HTML version deleted]] </div

Pathways SPIA Pathways SPIA

updated 14.1 years ago • Jing Huang

to do something like can be done on Microsoft Access merging the two files using the common unique identifier the snps. SNP Pval Fst snp001 0.0005 0.25 snp002 0.0003 0.75 snp003 0.0001 0.65 snp004 0.00001 0.3 snp005 0.00006...Any help with this in R will be greatly appreciated. Thanks. Avoks [[alternative HTML version deleted]] </div

updated 12.2 years ago • Voke AO

from the same patient assigned to different clusters - and thatÂ´s not what I want. I am trying to identify different classes between subjects, not biopsies. For the diff exp analyses, we dealt with this issue by adding the...artificial' data. Does anyone have an idea? Many thanks, Moritz [[alternative HTML version deleted]] </div

Clustering affy Clustering affy

updated 12.5 years ago • Moritz Kebschull

<div class="preformatted">Dear list, I would like to apply the Rank Products method in a two-color experiment on breast cancer data in order to identify differentially expressed genes between ER+ and ER- samples. I downloaded the R-package RankProd and tried to use the...like to apply the Rank Products method in a two-color experiment on breast cancer data in order to identify differential…

Cancer RankProd Cancer RankProd

updated 17.6 years ago • Eleni Christodoulou

been able to get the combination of Rraphviz and the other pieces to work under windows? And, what version of Visual Studio would be appropriate? I am really needing back compatibility for 32 bit R 2.11, so if there is an earlier

Rgraphviz PROcess GLAD Rgraphviz PROcess GLAD

updated 14.7 years ago • Gregory D.Rodd

is there a place where spade 1.8 is still available for download? -- output of sessionInfo(): R version 3.0.1 (2013-05-16) Platform: x86_64-apple-darwin10.8.0 (64-bit) locale: [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF

spade spade

updated 11.8 years ago • Guest User

are using   the same annotation for both. My question is how/where I can obtain the correct version of  EnsDb.Hsapiens for the transcriptome (ftp://ftp.ensembl.org/pub/release-86/fasta/homo\_sapiens/cdna

ensembldb ensembl release rnaseq salmon tximport

updated 7.9 years ago • emmak

with 16 GB RAM and used 9.7 GB RAM. The final .Rdata file has a size of 2.0 GB. Maybe, a future version of GEOquery could reduce both time and memory consumption. 2, Non-unique GEO platforms: I have also downloaded our...below). Sorrowly, this is not sufficient in this case (and probably other Affymetrix chips where two versions exist). Even though the Sample_data_row_count is different (12625 v…

hgu95a hgu95av2 GEOquery hgu95a hgu95av2 GEOquery

updated 19.9 years ago • Christian.Stratowa@vie.boehringer-ingel…

class="preformatted">Hi, I have a question about using sam method in siggenes package. My R version is 1.9.0 and my siggenes package version is 1.0.6. I took a look at the usage page for sam and I'm a little confused about...sam(data,cl) Then I got the following error: Error in data[, c(x,y)] : incorrect number of dimensions. Any advice on this will be…

siggenes siggenes

updated 21.2 years ago • saran.2.vardhanabhuti@gsk.com

Good day, my goal is to design fish probes for an uncultured bacterial species that is part of a microbiome. I do have the 16S sequence of the species and a dataset of V1-V2 16S amplicon sequences of the microbiome without taxonomic assignment. I want to use the DECIPHER package in R following the current documentation for FISH-probe design. I have to work around the fact that I don't have …

decipher FISH DECIPHER FISH-probe probe-design

updated 4 weeks ago • vreinmuth

I am new to R. I have clustered the samples (columns) using hclust function. Since there are a huge number of samples, 291, the sample names in the cluster tree is cluttered. Please suggest if i can zoom the cluster plot or what...average") >plot(hc_samples) Thanks in advance! Regards, S.Dhaarini [[alternative HTML version deleted]] </div

updated 16.7 years ago • dhaarini s

function will get you a reasonable answer. The genoset package has a better way to summarize copy number by gene, given a RangedData of gene boundaries. Please check out the end of the genoset vignette. Regards, Pete Haverty...List: > > Happy New Year! > > I have a question regarding mapping the gene to a copy number variations. > > I have affy 250 nsp m…

SNP Annotation probe affy biomaRt IRanges SNP Annotation probe affy biomaRt IRanges

updated 14.0 years ago • Peter Haverty

<div class="preformatted">Hi, I'm having a problem building a custom AnnotationDbi-style package using the SQLForge functions. It appears that something from the RSQLite package is disagreeing with the makeHUMANCHIP_DB function, such that there's an "attempt to write a readonly database". See below for a full transcript: > library('AnnotationDbi') Loading required package: Biobase …

oligo oligo

updated 17.5 years ago • Tim Rayner

somewhere I'm analysing new data from an Human Illumina HT-12 v3 BeadChip. I'm using BeadID as the identifier however the illuminaHumanv3BeadID.db package seems to be missing some of the Bead Ids from my top table list...what packages should I use to create my own annotation package? Many thanks Donia Session Info: R version 2.10.0 (2009-10-26) i386-pc-mingw32 locale: [1] LC_COLLATE=English…

Annotation Annotation

updated 16.1 years ago • Macartney, Donia

<div class="preformatted">In my version of siggenes, I don't see any variables called x and y that can be passed to the function sam. If RG.all contains all the data you wish to compare, you only need to pass this data.frame along with a vector of classlabels that identify which class each column of data belongs to. If you are doing a two-class unpaired analysis, this will be a vector of 0s…

Microarray Cancer siggenes Microarray Cancer siggenes

updated 22.0 years ago • James W. MacDonald

Hi everyone, I am one of the contributors of the [MesKit Bioconductor package](https://bioconductor.org/packages/devel/bioc/html/MesKit.html). We made some changes on the MesKit package few days ago and pushed to both the github and Biocondutor repo. However, no changes were found when we checked the Bioconductor landing page of MesKit. Although the latest version could be obtained when usi…

MesKit

updated 4.8 years ago • wangx555

in to many speed bumps. I'm trying to look at two CEL files (samples) and considering it is a small number of samples, I assumed the bare basic example from the manual would be sufficient but I run into the following problem...Error: number of cluster centres must lie between 1 and nrow(x)" Where would I define the cluster centres? Is this an issue with the CEL...clrmmResult <- crlmm(cel…

crlmm crlmm

updated 15.3 years ago • Ricardo Vidal

Incompatible phenoData object. Created a new one. I understand that as a not consistent number of rows between my experiment description file (241,500 probset ids) and number of rows in .CEL files (1,102,500 probes). When...it does that it resets the probsets id and starts numbering the rows from 1 to 1,102,500 and thus loosing track of probset ids. The point is that I need to know which probes …

cdf cdf

updated 15.9 years ago • marek piatek BI

Hi everyone, My experiment includes identifying DEGs in potatoes at various timepoints during drought when compared to the control (with no drought conditions...I have two varieties of crop - tolerant and susceptible. I have identified multiple DEGs across my experiment. Specifically, I have identified DEGs (1): unique to the Tolerant variety compared

heatm heatmaps

updated 3.7 years ago • axe880

<div class="preformatted">Dear biocondutors, Obviously the database files accessible at the refseq, gene or locuslink ftp sites do not contain all ids which can be uniquely identified via the ncbi web interface. Whrere can I find database files containing the rest? Query the RefSeq identifier "NM_032722" via NCBI in the gene database and it will return exactly one hit: C1orf170 Li…

updated 18.9 years ago • Benjamin Otto

gt; affydata AffyBatch object size of arrays=984x984 features (16 kb) cdf=Citrus (30395 affyids) number of samples=1 number of genes=30395 annotation=citrus notes= > mas5.eset<-mas5(affydata) background correction: mas...pmIndex, mmIndex)), ncol = 1) :matrix: invalid 'nrow' value (too large or NA) > sessionInfo() R version 2.9.1 (2009-06-26) x86_64-unknown-linux-gnu locale…

probe affy gcrma probe affy gcrma

updated 16.3 years ago • yuduanding

phenoDataFile) that I am trying to read in. The difference I noticed between the two R versions is that R 2.5 gives it the correct dimension 36 X 3 but R 2.7 reads it with dimensions 36 X 2. FileName Cell Sample 1356_0264_Kaliszewska_1396.plier

updated 17.5 years ago • daphne mouzaki RI

functionality bypasses the DAVID API, instead mimicking browser window interactions directly. The version number should be 1.7.1 or 1.8.1, (The latter is officially correct, but they are identical versions.) Building on this

Cancer DAVIDQuery Cancer DAVIDQuery

updated 15.5 years ago • Day, Roger S

3.14.0, I have the following script, but estimateDisp failed. However, when I run on an earlier version of edgeR, it works fine. Please see whether you can help to debug this.  > library(edgeR) > \#load(count\_mat) > \#16 samples

edger

updated 9.4 years ago • donghai.wang

to test GO terms association. I would like to know whether it is possible to set limits on the number of selected genes in GO term and the size of that term on my affy chip? For example, can I tell hyperGTest to skip testing...a GO term if the number of significant genes in that term is under, say, 3, or if there are more than 400 genes of that GO term on the chip? Currently...Is there such an …

GO GOstats GO GOstats

updated 17.7 years ago • alex lam RI

Binning grid too coarse for current (small) bandwidth: consider increasing 'gridsize' I use R version 2.9.2. Info about the data: AffyBatch object size of arrays=1002x1002 features (8 kb) cdf=Mouse430_2 (45101 affyids...number of samples=3 number of genes=45101 annotation=mouse4302 notes= Can I increase the 'gridsize'? The pdf's created also have...Bioscience Engineering: Cell and Gene B…

arrayQualityMetrics arrayQualityMetrics

updated 15.8 years ago • Koen Marien

functions that will show the difference? Thank you, Giovanni [[alternative HTML version deleted]] </div

updated 11.7 years ago • Giovanni Bucci

details: call: checkDBSCHEMA(dbconn, "BOVINECHIP_DB") error: invalid DB schema version (found 2.0, expected 2.1) ERROR: loading failed * removing '../data/bovinebtentrezg.db' Here is my sessionInfo()-Output: ============================== &gt...sessionInfo() R version 2.11.1 (2010-05-31) x86_64-unknown-linux-gnu locale: [1] C attached base packages: [1] stats graphics grDevices ut…

updated 15.6 years ago • Christian Kohler

The [https://bioc-release.r-universe.dev](https://bioc-release.r-universe.dev) repository syncs from your [bioc/packages.json](https://bioconductor.org/packages/json/3.22/bioc/packages.json) like so: ```r yml <- yaml::read_yaml("https://bioconductor.org/config.yaml") registry_url <- sprintf('https://bioconductor.org/packages/json/%s/bioc/packages.json', yml$release_version) bioc &a…

Bioconductor

updated 4 weeks ago • Jeroen

Recently I realized that my previous results done a year ago are dramatically different with updated version. I had the exact same input and code, which was for a bulk ATAC experiment with 6 paired samples. Out of around 150k peaks...8000 peaks had FDR<0.05 using version 1.28.5 while version >=1.33.11 had 0. I'm wondering if the changes in scaled weights that lead to this, and if so…

variancePartition

updated 20 months ago • Le

<div class="preformatted"> readVcf fails to load VCF files where alternate alleles containing breakends exist but no symbolic alleles. If any variant in the VCF contains a symbolic alleles, then the VCF does load correctly (including any breakend alleles - see example below). Reproduction steps: > library(VariantAnnotation) > readVcf("fail.vcf", "fake.fa") Error in .Call2("ne…

updated 12.2 years ago • Guest User