Bioconductor Forum

gt; all.raw AffyBatch object size of arrays=712x712 features (11889 kb) cdf=Zebrafish (15617 affyids) number of samples=3 number of genes=15617 annotation=zebrafish > all.mas5 <- call.exprs(all.raw,"mas5") Background correcting...p-values Doing PMA Calls Error in FUN(X[[4]], ...) : subscript out of bounds > sessionInfo() R version 2.1.1, 2005-07-10, i386-pc-mingw32 attache…

zebrafish cdf probe reposTools gcrma matchprobes simpleaffy zebrafish cdf probe gcrma

updated 20.4 years ago • Dick Beyer

not sure where to start. Thanks in advance for any pointers/scripts. Nathalie > sessionInfo() R version 2.11.1 (2010-05-31) x86_64-unknown-linux-gnu locale: [1] LC_CTYPE=en_GB.UTF-8 LC_NUMERIC=C [3] LC_TIME=en_GB.UTF-8 LC_COLLATE...Trust Sanger Institute is operated by Genome Research Limited, a charity registered in England with number 1021457 and a company registered …

Annotation annotate Annotation annotate

updated 14.2 years ago • nac

I have a data set with matched RNA-seq and DNA WGS, I notice many samples have an estimated copy number of 4 for about 70% to 80% of their chromosomes from the DNA sequencing analysis. [1]: https://www.cell.com/cell/fulltext/S0092...to make some value like the median fold change between samples the same. Could a more complicated version of it be developed in future? For example, it might loo…

edgeR DESeq2 Transcriptional Amplification

updated 6.7 years ago • Dario Strbenac

protein supplement and some received placebo. The design is unbalanced (the protein placebo numbers are not equal , also male and female are not the same number). At both times( before exercise and after exercise) the Transcriptomics...variation,...interactions) Thank you so much ion advance Regards Pari [[alternative HTML version deleted]] </div

limma limma

updated 12.4 years ago • Fazelzadeh, Parastoo

<div class="preformatted">I have an odd problem that I cannot seem to figure out. I have a set of CEL files in a directory, which I read using the ReadAffy() command. Then I run the rma command to preprocess. > Data <- ReadAffy() > alldata <- rma(Data) I've done this many times before without problems. However, when I try to use text instead of numbers for s…

cdf reposTools affy PROcess cdf reposTools affy PROcess

updated 19.7 years ago • Jeff Lande

NOT FOUND Erreur dans getBM(attributes = c("external_gene_id", "go_biological_process_id", : Number of columns in the query result doesn't equal number of attributes in query. This is probably an internal error, please...human)[19,] name description 19 biol_process <na> > > sessionInfo() R version 2.7.0 (2008-04-22) i386-pc-mingw32 locale: LC_COLLATE=Fre…

GO biomaRt GO biomaRt

updated 17.2 years ago • J.J.P.Lebrec@lumc.nl

snp.gr.rda", package="BubbleTree")) It has the error message: Error: bad restore file magic number (file may be corrupted) -- no data loaded In addition: Warning message: file ‘cnv.gr.rda’ has magic number '<'   Use of save...versions prior to 2 is deprecated   I also tried my own dataset vc.df = read.csv("F5.snp..inputBT.csv", header=T, sep=",") …

software error

updated 10.0 years ago • jial2

Y and Z and I'm comparing Y vs H and Z vs H (H is the control group). First, I did all that for with version hg38 and everything went fine. For some purpose, I needed to redo everything using the hg19 version of the genome. At...other data sets and also happens every now and then - particularly with some comparisons where the numbers are pretty similar (pair wise comparison between two conditions…

diffbind

updated 6.5 years ago • melnuesch

with: eb<-ebayes(fit) the data from ebayes is later used in the toptable function: toptable(number=100,genelist=list[,],fit=fit,eb=eb,adjust="fdr") When I make this analysis I get a list of 82 genes for cond1 that has a B-value...And make the function calls like the procedures above except the toptable where I specify the coef number to be the condition which I want to investigate. Th…

Pathways limma Pathways limma

updated 22.1 years ago • Marcus

Regards, Michelle R version 2.13.2 (2011-09-30) Copyright (C) 2011 The R Foundation for Statistical Computing ISBN 3-900051-07-0 Platform: i386-apple...fit,contrast.matrix) > fit2=eBayes(fit2) > results1 <-topTable (fit2, coef=1, p.value=0.3,number=nrow(fit2)) > dim(results1) [1] 889 8 > results1 <-topTable (fit2, coef=1, p.value=0.5,number=nrow(fit2)…

GUI GUI

updated 13.4 years ago • michelle_low

<div class="preformatted">Hi, Nathan, I haven't seen messages like these. The warnings suggest that numbers are being interpreted as strings, and converted to factors, but I can't imagine why that would happen. Can you send along your sample sheet, and the first few lines of your peaks files? I'll see if I can reproduce it. Also, can you let me know the sessionInfo() and operating syste…

DiffBind DiffBind

updated 12.5 years ago • Gord Brown

I used the TTD database to identify a list of proteins that I want to highlight in a KEGG pathway map. From this database I can extract the UniprotKB AC...I used the TTD database to identify a list of proteins that I want to highlight in a KEGG pathway map. From this database I can extract the UniprotKB AC/ID for each protein. For example for HDAC1, this would be HDAC1_HUMAN. On the Uniprot web…

ID Uniprot EntrezID

updated 3.6 years ago • tom.kloter

Dear Florian, I would like to show the common name of genetic elements and not the UCSC's identifier (I think it is what we see). In addition, I would like to know if it is possible to have the color of genetic elements...Dear Florian, I would like to show the common name of genetic elements and not the UCSC's identifier (I think it is what we see). In addition, I would like to know if it is …

gviz ucsc

updated 10.7 years ago • Tiphaine Martin

Dear Community, briefly in a current project i tried to implement the R package motifbreakR, in order to identify putative SNPs from somatic variant calling, that could cause an "important" disruption in TF-binding sites. The first part of my code chunk, is for reading the SNPs included in the relative vcf file i tried as an initial example: <pre> library(motifbreakR) library(BSgenome) …

motifbreakR vcf snps motif analysis

updated 7.5 years ago • svlachavas

dear list, i would like to produce a GO graph where the labels of the nodes are formed by the GO identifier and the GO term and these two pieces of information appear in two different lines within the node, in order to draw...shows the GO ID. anyone has tried this or has an idea how it could be done ? my sessionInfo(): R version 2.6.0 (2007-10-03) x86_64-unknown-linux-gnu locale: C attached…

GO graph GO graph

updated 17.8 years ago • Robert Castelo

<div class="preformatted">Hi all, Hoping someone could give me a bit of direction here. I have a set of genes which are all members of the same pathway. I want to identify if there are any transcription factor binding sites (TFBS) in the "promoters" (so far defined as 5kb upstream of the TSS...bit of direction here. I have a set of genes which are all members of the same pathway. I want…

Transcription convert biomaRt Transcription convert biomaRt

updated 13.8 years ago • Davy

<div class="preformatted">Hello List Perhaps someone could help me with this. I am annotating some 200 genes with the org.Bt.eg.db package. The identifier I have for the genes is and Ensembl ID (e.g. ENSBTAG00000009012). I am attempting to return the ENTREZ id with the following...someone could help me with this. I am annotating some 200 genes with the org.Bt.eg.db package. The identifier …

updated 14.4 years ago • Iain Gallagher

pipermail/bioconductor/2011-January/037449.html And the answer was to use clustering for identifying the G1,S,G2 population. I have tried to find some publication where this method was used for cell-cycle analysis...grateful to you for any help or suggestion. Kind regards, Dmytro -- output of sessionInfo(): R version 2.15.0 (2012-03-30) Platform: i686-pc-linux-gnu (32-bit) locale: [1] LC_C…

Clustering flowStats Clustering flowStats

updated 13.0 years ago • Guest User

data structure to set up correctly. I have imported the CEL files in with oligo, and ctrlIdx can identify regions correctly. I just can't get it to estimate percent methylation Andrew -- output of sessionInfo(): R version 2.15.2

BSgenome affy BSgenome oligo charm BSgenome affy BSgenome oligo charm

updated 12.8 years ago • Guest User

padj < 0.1) when I include all 6 groups. When I remove group F, only 239 DEGs (padj<0.1), were identified. The question is, which method should I use in this case. My code: ### Get the DEGs between group A and B, where dds\_6groups...padj),] res_1_p10<-res_1_rmNA[(res_1_rmNA$padj<0.1),] rownames(res_1_p10) #373 DEGs identified</pre> ### recalculate d…

deseq2 rna-seq

updated 7.6 years ago • Raymond

at Longwood, 342 Longwood Ave, Boston MA, 23-24 Feb 2009. For students traveling to Boston, a small number of discounted hotel rooms has been arranged; discount expires 6 February. Fees are 650USD academic, 1300USD commercial...to stvjc@channing.harvard.edu Registration is limited to 25 students. [[alternative HTML version deleted]] </div

updated 16.9 years ago • Vincent J. Carey, Jr.

<div class="preformatted">Hi, I am trying to create a GRanges list object for all the features of a transcript database created from the GENCODE gtf file. I have created GRanges object for the features "exons","genes","transcripts","introns". When I try to combine these individual objects into a GRangesList, I get the following error: >grl<-GRangesList("genes"=genes.gencode,…

TranscriptDb TranscriptDb

updated 11.8 years ago • Kalyan K Pasumarthy

controls, applying log, selecting genes over a certain fold change etc.). I end up with different numbers of genes... I have done A LOT of debugging (including doing the same actions manually in excel :o/ ) and am quite convinced...Is there anyway to better approximate the MAS5 scaling? Thanks! Liat. [[alternative HTML version deleted]] </div

Normalization affy Normalization affy

updated 13.4 years ago • Liat Shavit Grievink

how good a replicate is? I have tried using various outlier elimination methods to count the number of genes being eliminated for each replicate. I have found this to be reasonable for accounting global differences...Thanks, Richard Park Computational Data Analyzer Joslin Diabetes Center [[alternate HTML version deleted]]</div

updated 22.6 years ago • Park, Richard

Affy human gene expression arrays (HG-U133_Plus2.1) CEL files representing a treated sample over a number of time points. I'd like to compare the expression of these files not just on the genes they probe but on the exons. I know...than whole genes? Or am I completely wasting my time on this? Peter [[alternative HTML version deleted]] </div

probe affy probe affy

updated 16.2 years ago • Peter Saffrey

<div class="preformatted">Using the latest version of EBImage and ver 8:6.6.9.7-5 of ImageMagick (debian package) several EBImage operations fail. In particular, cropping an image with: a<-readImage("xxxxxxxx") a[1:120,50:120] # fails with "incorrect number of dimensions"] I can get cropped images by doing: a[1:120,50:120,1] # display gives correct region with a red mask a[1:120,50…

EBImage EBImage

updated 14.3 years ago • Michael Cole

and using beadarray's calculateDetection, you get an error: Error in negControls[, i] : incorrect number of dimensions This appears to be due to the default drop to lower dimension, in this line (in beadarray:::getNegatives...which should be: nData = exprs(BSData)[nIDs, ,drop=FALSE] Cheers, Cei > sessionInfo() R version 2.8.0 (2008-10-20) i386-apple-darwin8.11.1 locale: C att…

updated 16.9 years ago • Cei Abreu-Goodger

<div class="preformatted">Hi, How could I efficiently construct a PLINK map file from scratch using a large list of SNP IDs? Unfortunately I don't have the original map file for our data. I've tried the batch search option at the NCBI SNP DB but the output files are not so practical to use. I've also tried to annotate the list from within WGAviewer, which works well for a small list of SNP…

SNP annotate SNP annotate

updated 17.2 years ago • Fabio Sanchez

Limma, using CL_scrambled as the ref in the design matrix. Unfortunately there are a substantial number of differentially expressed genes between the CL and CL_scrambled which will potentially confound the experiment...vs CL_scrambled ? I'd appreciate any advice that you can give. Bryony [[alternative HTML version deleted]] </div

limma limma

updated 15.2 years ago • Lloyd, Bryony

<div class="preformatted">Dear Sir or Madam, I am interested in using Bioconductor to analyze and compare some data Ive recently acquired and was wondering if you could help direct me to an appropriate analysis package. I have two sets of data, from two separate groups of AML patients. One set is of 96 patients, the other set is of 178 patients, and I have sequencing data for both groups…

Sequencing Sequencing

updated 13.7 years ago • Javerjung Sandhu

GeneID = geneIDs, GeneSymbol = geneSymbols, GeneName = geneNames, : arguments imply differing number of rows: 34760, 35556, 1 > summary(geneIDs) Length Class Mode 34760 character character > summary(geneNames) Length...Mode 35556 character character What should I do? Cheers Joel [[alternative HTML version deleted]] </div

cdf cdf

updated 11.5 years ago • Joel Ma

<div class="preformatted">Dear List, I have several biological replicates affy arrayes (a simple one group 4 arrayes), and tried to use eBayes to get the differentially expressed genes. The topTable ranked the genes by B statistics, which mixed over- expressed genes and under-expressed genes. My question is how I should separate the over and under expressed genes from topTable results. My …

affy affy

updated 16.2 years ago • Roger Liu

Hello, I would like to convert a Binary CEL file to txt file, which has same strunktur as version 3 in HG_U133 CEL files (charachter File). The result muss a table with "probe set name", "probe number", "intensity" and "mean

convert convert

updated 20.7 years ago • Mohammad Esad-Djou

<div class="preformatted">Dear Sir or Madam, I am interested in using Bioconductor to analyze and compare some data Ive recently acquired and was wondering if you could help direct me to an appropriate analysis package. I have two sets of data, from two separate groups of AML patients. One set is of 96 patients, the other set is of 178 patients, and I have sequencing data for both groups…

Sequencing Sequencing

updated 13.7 years ago • Javerjung Sandhu

div class="preformatted">Hello, I use R version 2.9.2 under MacOSX Tiger, and the oligo (1.8.3), oligoclasses (1.6.0) and pd.hugene.1.0.st.v1 (2.4.1) packages. I imported...included in each probesets (roughly a 4:1 ratio between probes and summarized probesets). The median number of probes by probesets is supposed to be 26 with that specific technology. Does someone have an explanation or a …

oligo oligo

updated 16.2 years ago • Thibault Helleputte

different GO terms and genes corresponding to the difference of the GO term since I used AGI number as input from Arabidopsis GENE ST1.1 array. Bing Wageningen University [[alternative HTML version deleted]] </div

GO GO

updated 11.9 years ago • Bai, Bing

Hello: I have a list of Kegg Orthology (K) numbers that I would like to covert from K to entrezID to use clusterProfiler package. Currently, I am trying to install the...biocLite.R") biocLite("org.Hs.egPATH”) 1: package ‘org.Hs.egPATH’ is not available (for R version 3.3.1) 2: In install.packages(update\[instlib == l, "Package"\], l, repos = repos,  :   installation of …

org.Hs.egPATH

updated 9.3 years ago • ladypurrsia

Hi all, I am working with Agilent microarray data and trying to extract only the accession numbers from the output probe annotation. Basically I have a column detailing the probe as follows: ref|NM_004564|ref|PET112L...R/Bioconductor and would appreciate if someone can help. Thanks. Hari [[alternative HTML version deleted]] </div

Microarray Annotation probe Microarray Annotation probe

updated 16.5 years ago • Hari Easwaran

BIOC: Quality control information for rat2302 Date built: Created: Thu Mar 15 18:25:07 2007 Number of probes: 31099 Probe number missmatch: None Probe missmatch: None Mappings found for probe based rda files: rat2302ACCNUM...Feb-2007 Quality control information for rat2302Geno Date built: Created: Fri Mar 23 14:18:24 2007 Number of probes: 31099 Probe number missmatch: None Probe m…

Annotation GO rat2302 probe Biobase annotate AnnBuilder PROcess Annotation GO rat2302

updated 18.7 years ago • Asta Laiho

Good evening BioConductor ListServ, I am interested in using edgeR to generate a single list of genes differentially expressed between treatment and control and either of two time points (similar to User Guide section 3.3.3). I have generated what I think is the correct contrast and model, but I am confused by the number of genes at FDR<0.1 on the output list compared to the number of gen…

edgeR

updated 10.9 years ago • Matt McNeill

Hi,  I tried to analyze RNA-seq data using DESeq2. I have 2 sample conditions: 1 mg/mL and 2 mg/mL My control sample is 0 mg/mL.   When I tried to identify differentially expressed genes between 1 mg/mL and 0 mg/mL using standard analysis I observed: _out of 12632 with nonzero total read count adjusted p-value < 0.05 LFC > 0 (up)  &…

rnaseq deseq2

updated 8.2 years ago • Letícia

I recently noticed that the bplapply seems work differently from the older version. For example, if I want to do a number of lm ```r library(BiocParallel) # simulate some data for 10000 regressions N = 10000 nobs...I recently noticed that the bplapply seems work differently from the older version. For example, if I want to do a number of lm ```r library(BiocParallel) # simulate some data fo…

BiocParallel

updated 4.1 years ago • Wu, Hao

are significantly more or less abundant in the healthy vs diseased samples. I tried running the new version of DESeq (1.8.3) on both a Mac and a PC running the latest version of R (2.15). Both versions give a strange result, where all...samples). I asked a colleague to help me with the analysis, and he ran the analysis on an older version of DESeq (1.4), using the estimateVarianceFunction com…

Genetics graph DESeq Genetics graph DESeq

updated 13.5 years ago • Flavia Nunes

none of the alignments have been assigned. On the other hand, if I modify my SAF file to remove the version number from the chromosome seq-id, I see ~25% of the alignments assigned. I think this is a bug in `featureCounts` and present...at least in an older version v2.0.2 and perhaps even earlier. I read in an older post that this could be because of line endings. In my case, all line

featureCounts subread Rsubread

updated 20 months ago • vkkodali

Dear list, a new package called 'qpgraph' has recently become part of the current development version of Bioconductor (version 2.4). 'qpraph' aids in reverse engineering molecular regulatory networks from microarray...They are useful for learning undirected graphical Gaussian Markov models from data sets where the number of random variables p exceeds the available sample size n as, for instance…

Microarray Network Microarray Network

updated 16.8 years ago • Robert Castelo

design) Error in dispCoxReid(y, design, offset = offset, ...) : no data rows with required number of counts If I run the estimateGLMCommonDisp() function in my dataset it works. If I run the example from the Documentation...Does anyone have a clue of what I am doing wrong? Thanks very much, Fernando sessionInfo() R version 2.13.0 (2011-04-13) Platform: x86_64-pc-mingw32/x64 (64-bit) l…

edgeR edgeR

updated 14.6 years ago • Biase, Fernando

<div class="preformatted"> I downloaded a number of SNP 500K data from GEO to run with CRLMMM. The following CEL files specified by GEO as NspI files. > fulFileNames [1...div class="preformatted"> I downloaded a number of SNP 500K data from GEO to run with CRLMMM. The following CEL files specified by GEO as NspI files. > fulFileNames...recalibrate = recalibrate, : Al…

SNP crlmm SNP crlmm

updated 16.5 years ago • mcoyne@boninc.com

started to use R for data analysis. Now, I am trying to analyze our ChIP-seq data using DiffBind to identify genomic regions that are commonly or differentially bound by one transcription factor and its mutant. I have been...A) or mutant (condition B) and of the common regions. (Eventually, I will perform motif analysis to identify transcription factor binding motifs enriched in each condition.) …

diffbind

updated 10.6 years ago • ruka.setoguchi

I'm new to ATAC-seq analysis and have recently been trying to use DiffBind to systematically identify differential peaks that I've been seeing by eye when looking at macs2 output in IGV. I have two conditions in triplicate...free regions for each condition as well as on the entire dataset. When looking in IGV I can identify peaks in the pooled dataset that are unique to one condition or the other…

DiffBind ATACSeq

updated 2.4 years ago • Nebat

Hi all, I am working on an RNAseq experiment where we have three experimental doses and a control. I have completed the analysis using the dose as a group assignment, but I am curious about genes which have a linear relationship across the gradient of doses. My initial approach was to identify DEGs which changed in the same direction in the pairwise dose vs. control contrasts, but it appears t…

edger continuous regression

updated 6.9 years ago • emb13

like ensembl, because I want to combine the microarray data with Chip-Seq results. I want to identify the differentially expressed lncRNAs that are also regulated by my target transcription factor. My problem is...Chip-Seq can provide a common identifier like ensembl, but the lncRNA annotations are from different database, making it impossible to compare the two

re-annotation affymetrix microarrays chip-seq affymetrix mouse gene arrays

updated 7.1 years ago • 2323982403

Hi everyone, I’m testing for GO categories enrichment using goseq (version 1.32.0) under two different approaches (as described below) and I’m getting different numbers of genes per GO category...binding MF</pre> Even if I force the inclusion of genes without categories in the test, the number of genes per category is the same! <pre> > GO.hiper = goseq(pwf, "bosTau4",…

goseq biomart

updated 7.5 years ago • frezende

for the small pvalues. I test here on golub data, and I don't have the same differential genes number when I observe the delta tables (delta.table for samr and sam.out at mat.fdr for siggenes) for a FDR 0% (250 are differential...9 with siggenes package). On my personnal data, I observe the same difference in differential gene number at FDR 5%. I also observe the same s0, but not the same pi0, in…

siggenes siggenes

updated 17.6 years ago • Cécile Laurent

<div class="preformatted">Dear Zhijin, (I sent the following in May and June to the list (worded slightly differently) but did not receive a reply. I would appreciate it if you, or someone on the list could could clear up this problem) I am noticing a large change in the absolute values of intensity measurements For the same probeset and and array normalized w…

Cancer gcrma Cancer gcrma

updated 17.4 years ago • Richard Friedman

each in vivo). In fact DESeq2 performed better than Transit with Mann-Whitney hypothesis testing to identify internal control effects for specific genes. Question is whether DESeq2 is in fact appropriate for the following...and have read that the DESeq2 model can handle these conditions, though in the TnSeq dataset the number of genes where such occurs is 2-5X that of our RNAseq datasets. A seco…

DESeq2

updated 7 months ago • Lynn

<div class="preformatted">> Date: Sun, 2 Jan 2005 14:05:15 -0800 (PST) > From: "Fangxin Hong" <fhong@salk.edu> > Subject: [BioC] A question about Limma > To: bioconductor@stat.math.ethz.ch > Message-ID: <1867.66.75.240.64.1104703515.squirrel@66.75.240.64> > Content-Type: text/plain;charset=iso-8859-1 > > Hi Biocondu…

PROcess Microarray limma

updated 2.6 years ago • Gordon Smyth

in vitro data about a specific microRNA that is related with stemness, I analyzed a small number of relative microarray samples, based on two conditions (3 reps each)-one of the major downstream goals, was to identify

mroast camera gene set testing

updated 5.2 years ago • svlachavas

Hello everyone,   I have available 17 000 variables (SNV frequencies, a certain number of zeros) for 40 patients. Each patient is represented by its response to a treatment : 13 responses, 27 no-responses. I...Hello everyone,   I have available 17 000 variables (SNV frequencies, a certain number of zeros) for 40 patients. Each patient is represented by its response to a trea…

adaptive-lasso snv biomarkers cv glmnet

updated 9.0 years ago • crichard

An opening for a PhD, or MSc+PhD, student position is available in the group of Robert Hoehndorf at the King Abdullah University of Science and Technology, Thuwal, Saudi Arabia. Group website: http://borg.kaust.edu.sa Research area: Machine learning and ontologies in biology Location: Thuwal, Saudi Arabia Application deadline: Fall 2017 Project description: Some recent advances in mac…

job MSc PhD machine learning Job

updated 8.2 years ago • senaykafkas

would like to perform statistical analysis on the normalized intensities of the individual probes to identify those probes that are significantly regulated between different conditions or treatments. How to perform the...gt; > Thanks in advance.. > > Regards, Suresh >     [[alternative HTML version deleted]] > > > &g…

Normalization probe affy limma Normalization probe affy limma

updated 14.0 years ago • suri ghani