Bioconductor Forum

design = ~ Particle + BMI + Diagnosis) dds$Diagnosis <- factor(dds$Diagnosis, levels = c("PCOS","non-PCOS")) dds$BMI <- factor(dds$BMI, levels = c("Lean","Obese")) dds$Particle <- factor(dds$Particle, levels = c("MP","FFD","EV")) dds...value = contr.funs[1 + isOF[nn]]) : contrasts can be applied only to factors with 2 or more levels</pre> I'm also looking to ma…

deseq2 multiple factor design contrast

updated 7.5 years ago • russell.stewart.j

<div class="preformatted">Hello all, I am new to bioconductor and I am running into a couple of problems converting a marrayNorm object to an exprSet object. I convert the marrayNorm object to an exprSet using the following: library("convert") xEset <- as(marrayNorm object, "exprSet") The problem is that there does not seem to be any probe level information in the exprSet i.e. &a…

Cancer probe convert Cancer probe convert

updated 19.4 years ago • Daniel Brewer

Predicted outcome distribution for test set: B O 102 98 history of feature selection in cross-validation available; use fsHistory() it includes results of each CV step, but it is wrapped up fairly tightly. You have to use...RObject at two levels, first for the CV-generated object, second at the CV-step level ... here are the first two steps for the example > lapply(RObject...model.…

Network Classification Network Classification

updated 15.1 years ago • Vincent J. Carey, Jr.

and the KEGG ID. When I feed this to the buildGOmap function, I get the error: *Error in names(object) <- nm : 'names' attribute [15883] must be the same length as the vector [0]* I have been getting an error that I am unable...5 GO:0016887 PA0001 6 GO:0006260 PA0001 > Pa_GOMap <- buildGOmap(Pa_GOterms) Error in names(object) <- nm : 'names' a…

clusterProfiler

updated 22 months ago • mello-vieira

1:10], Hsapiens, upstream=300, downstream=0) Error in .getOneSeqFromBSgenomeMultipleSequences(x, name, start, NA, width, : sequence chr19 not found In addition: Warning message: In .Seqinfo.mergexy(x, y) : The 2 combined objects have...no sequence levels in common. (Use suppressWarnings() to suppress this warning.) # Change chromosome naming style: > seqlevelsStyle(Hsapiens...…

bsgenome genomeinfodb transcriptdb

updated 11.0 years ago • Diego Diez

to load files from Cytek Aurora using read.FCS(). I keep getting the error that [filename] "is not a valid file". Filename has backslashes, so I changed the names to rid them of that. Now, I can get read.FCSheader() to work but not read.FCS

read.FCS read.flowSet

updated 2.6 years ago • Pilid

<div class="preformatted">I've gotten closer to getting a working yeast annotation package for the Affymetrix YEAST 2.0 chip. I was able to procure the proper ORF ids and the probe ids, and from there I used yeastPkgBuilder within AnnBuilder to create a package. It ran for a few hours and terminated with the following error: Error in readLines(con) : cannot open the connection From wha…

Annotation GUI Yeast probe Annotation GUI Yeast probe

updated 20.8 years ago • Jacob Michaelson

I have done all the possible comparisons from the results function, specifying which experiments must be compared to define the numerator and denominator of the fold change relation. Now I'm wondering if it is possible to...it is possible to do it, but in some sort of separate way, it is possible to plot the expression levels of a specific gene through the conditions, section 1.5.2 and figure 2,…

deseq2 standard deviation

updated 9.7 years ago • rafa.rios.50

I have ChIP-seq with two conditions. In condition A, there should a lot of peaks (normal binding). In condition B, there should be none (no binding). Calling peaks with MACS confirms this. When you perform differential binding analysis, you would expect most of the significant peaks to be up in condition A. However, I get half the peaks up and half down. That does not make sense. I am using Diff…

diffbind

updated 10.2 years ago • igor

Sequence unavailable CBL 3;1;2 ENST00000634301 HGNC:1541 ``` So, the column names don't seem to be assigned in the correct order?! Furthermore, there is "Sequence unavailable" and HGNC:1541" instead of cDNA

annotation

updated 5.4 years ago • sarah.sandmann

Owner/Desktop/Data/mydata2"), full.names=TRUE), read.FCS) > as(frames, "flowSet") Error in names(from) <- paste("V", seq(1, length(from)), sep = "") : 'names' attribute [2] must be the same length as the vector [0] > sessionInfo() R version

updated 16.9 years ago • Steve Lauriault

class="preformatted">hi, I would like to easily query the weight (or label) of an edge given its name. e.g. suppose I have a graph 'g' whose nodes are labeled A1, A2, ... I want to do something like: getEdge(g, "A1~A3")$weight Any suggestions

graph graph

updated 15.6 years ago • Gustavo Lacerda

Hello, I’m new to this so sorry if any of this is obvious but I would really appreciate any help. I have 6 cancer cell lines, two of each of the following subtypes: mesenchymal, proneural, classical. I want to find differentially methylated positions/regions, and have tried using limma to compare each subtypes in a contrast matrix but this generates no significant results. This is not totally …

minfi methylationArrayAnalysis

updated 4.7 years ago • chay

csv) in a bioinformatic context. I wonder, if there is a convention on how the "features" are named for DESeq2 csv outputs. In one of my sample datasets for genes for example, genes are named with "geneName.gene". Would an...example for CDS be named "cdsName.cds"? Is the .gene an error and the name column would normally contain only the feature name? Thanks in advance

deseq2 gene format

updated 6.4 years ago • miriam.mueller

Science will develop biomarkers for project teams, provide a feasibility assessment and validation of approach, provide a centralized biomarker analysis capability for clinical samples, and provide early clinical...for the exploration of NGS datasets \* Accountable for NGS biomarker data generation, validation and results/report delivery within AZ Oncology project and disease area teams. \*…

cancer translation ngs genomics Job

updated 10.7 years ago • jhjohnsn

tabular file ('", getPathname(this), "'): ", ex$message) at value[[3]](cond) at tryCatchOne(expr, names, parentenv, handlers[[1]]) at tryCatchList(expr, classes, parentenv, handlers) at tryCatch({ at verify.TabularTextFile(this...In read.table(3L, header = TRUE, colClasses = c(NA_character_, NA_character_, : not all columns named in 'colClasses' exist 3. I tried it also by using the…

cdf cdf

updated 15.5 years ago • Ivanek, Robert

I want to change two things in this cnetplot 1. Exclude pathways in the graph 2. Providing gene names instead of the IDs   __1. __Using the example: <pre> require(dplyr) head(kegg@result) %>% select(Description, setSize) Description...__2. __using the example Instead of the ids (such as `` 6891 ``) I want to show the gene names wh…

clusterprofiler pathway analysis pathways

updated 7.5 years ago • Mr.RB

We have recently published a _F1000Research_ workflow for low-level analyses of single-cell RNA-seq data: http://f1000research.com/articles/5-2122/v1 It covers basic steps including quality

scran scater single cell Tutorial

updated 9.3 years ago • Aaron Lun

it gives me result :- Note: http://www.bioconductor.org/CRANrepository does not seem to have a valid repository, skipping Note: http://www.bioconductor.org/repository/release1.3/package does not seem to have a valid...skipping Note: http://www.bioconductor.org/repository/devel/package does not seem to have a valid repository, skipping Note: http://www.bioconductor.org/data/metaData does not seem…

updated 21.6 years ago • rashi

error printed was: ``` downloading 1 resources retrieving 1 resource Error: failed to load resource name: AH32002 title: E001-H3K4me1.fc.signal.bigwig reason: 1 resources failed to download In addition: Warning messages

DFP

updated 4.4 years ago • hxwanghxw

Dear all, I am trying to map gene names to x y coordinates of probes in celfiles. My celfiles belong to gpl1339(S.aureus). I have some gpl1339 annotation files

microarray probe

updated 10.7 years ago • nazaninhoseinkhan

packaged somewhere. ``` library(tidyverse) library(rhdf5) read_ad_df <- function (file, name) { x_attrs <- h5readAttributes(file, name) ## check requested entry is a dataframe ## TODO: do we need to check encoding-version...lt;- unlist(x_attrs[c("_index", "column-order")], use.names=FALSE) ## load the factor levels x_levels <- h5re…

rhdf5 HDF5Array anndata SingleCellExperiment

updated 3.3 years ago • merv

pkgDesc <- lapply(package, packageDescription) if (length(package) == 0) stop("no valid packages were specified") basePkgs <- sapply(pkgDesc, function(x) !is.null(x$Priority) && x$Priority == "base") z$basePkgs...lt;- package[basePkgs] if (any(!basePkgs)) { z$otherPkgs <- pkgDesc[!basePkgs] names(z$otherPkgs) &am…

cdf cdf

updated 15.9 years ago • sneha patil

<div class="preformatted">Dear Benno, It makes perfect sense to remove from your Illumina analysis probes which seem to be entirely unexpressed throughout your experiment. This is a phenomena which is especially noticeable with Illumina arrays. However, to use this strategy, you must remove probes entirely, not selectively for some arrays but not for others. The simplest and probably the…

limma beadarray limma beadarray

updated 17.9 years ago • Gordon Smyth

underlying mechanisms of observed data results. Closely work with molecular biologist for target validation. __Minimum Qualifications:__ * All applicants must have a PhD in genetics, biology, bioinformatics, or closely related

rna-seq Job

updated 7.1 years ago • Jeremy Leipzig

tools. The input data are counts with DESeq2 normalization. It seems to work pretty well at gene level but not so smooth with isoform level analysis.  With one dataset, I got an error while running PodiumChange as below...PodiumChange(det.126Vs128, comparison = 'any') Error in tapply(zzM, repvect, mean) : arguments must have same length__ With another dataset, I got stuck at IsoMode…

masigpro

updated 8.2 years ago • xin.zhou

Hello everyone, I have an experiment with a 2 x 2 factor design, with condition having two levels (N vs NN) , and treatment having control (C) and stress (S) levels. I want to analyze the interaction effect so I run ```r design(dds...Therefore, to analyze the interaction I run ```r res1 <- results(dds_pol_nod, name = "conditionNN.treatmentS") ``` where by reading DESeq2 vig…

DESeq2

updated 3.5 years ago • mmartinez

which are the genes di erentially expressed in the laz T36 vs laz T0 : > targets SlideNumber Name FileName Cy3 Cy5 Moment 1 1 chip1 chipZ10.gpr pet0 laz0 T0 2 2 chip2 chipZ20.gpr pet0 laz0 T0 3 3 chip3 chipZ30.gpr pet0...pet36 laz36 T36 >design <- modelMatrix(targets, ref = "pet0") Found unique target names: laz0…

updated 13.9 years ago • sara domingos

colnames(design.gain1q)=c("Normal1q", "Gain1q") > contrast.matrix=makeContrasts(Gain1q-Normal1q, levels=design.gain1q) > fit2=contrasts.fit(fit, contrast.matrix) Then I get the message: Warning message: In contrasts.fit...fit, contrast.matrix) : row names of contrasts don't match col names of coefficients Remaining code: > fit2=eBayes(fit2) > results=topTable…

updated 17.0 years ago • Martin McCabe

box in the heatmap with ComplexHeatmap ideally I would like to create a block annotation with the name of the sample in it but so far I wasn't able to do it. Also which RGB color is the best to have blue and red and not purple-bluish...simple_anno_size = unit(2, "mm") ) a <- Heatmap(t(mydata), name = "z score", #title of legend …

r rnaseq complexHeatmap annotation

updated 5.5 years ago • camillab.

div class="preformatted">Hi Gordon, For my experiment, I have three levels of factors for genotype ("B2, "Ein40","Ein9") and two levels of factors as treatment ("Sun", "Shade"). I did a nested interaction method...counts) <- counts$gene counts <- counts[,-1] head(counts) counts[is.na(counts)] <- 0 names(counts) summary(counts) sort(colSums(counts)) counts <- counts…

updated 13.0 years ago • upendra kumar devisetty

query': Failed to collect lazy table. Caused by error in >db_collect(): >! Arguments in `...` must be used. >X Problematic argument: \ ..1 = Inf i Did you misspell an argument name

sesameData sesameDataCache sesame ExperimentalHub

updated 2.1 years ago • alos_diallo

data - the result of which is that the data now consists of a single file containing just the probe names and a single value for each adjusted sample. I want to filter out the non-detected miRNA as per the "filterMicroRna" function...file for each adjusted sample and manually adding back in the columns that I lost...I'm sure there must be an easier way. Any input would be greatly appreciated, …

miRNA probe AgiMicroRna miRNA probe AgiMicroRna

updated 15.4 years ago • Segal, Corrinne

from specifications. 7. Prepare documentation of completed analyses and present to team lead. 8. Must be able to handle multiple long term projects simultaneously and be able to budget time effectively. QUALIFICATIONS...or a Physical science, with a strong background in applied data analysis required. Masters level candidates preferred; Must have at least 1 year of programming in R, SAS or MATLA…

Epigenetics Annotation Network Epigenetics Annotation Network

updated 13.8 years ago • Guest User

Dear communities, I want to compute P/A calls at gene-level probesets so that it can be utilized for removing unexpressed probe after rma (target = core). As far as I'm concerned, oligo

pd.hugene.1.0.st.v1 oligo AffymetrixChip

updated 3.5 years ago • Yang Shi

not use argument "readable = TRUE" like "enrichGO" function. I have to translate the gene ID to gene name manually. Could you please help me fix this problem? Thank you

annotation

updated 6.9 years ago • huangzhiguang2016

files , but, the PGF/CLF were not useful in bioConductor packages for affy Exon/Gene type arrays ,namely: oligo & XPS as they require annotation file in csv format. I tried the annotation csv file from Affymetrix and after...annotation columns. Thus xps will not read these annotation files. >Alternative annotation files must contain exactly the same columns as >the Affym…

Annotation cdf probe affy oligo xps DOSE Annotation cdf probe affy oligo xps DOSE

updated 15.0 years ago • branislav misovic

related to computer science, statistics, or genetics   __Technical skills:__ Required: High-level of programming capability and experience Desirable: some basic knowledge of statistics, genetics, and computational...how to apply: <http://unc.peopleadmin.com/postings/111125> Open until filled. All applications must be received through the UNC application system

R genomics statistics Job

updated 8.8 years ago • radel

div class="preformatted">Dear Servin, You are mis-interpretting a little what the column names are intended to represent. They are names associated with the arrays, not with files or channels. All the data matrices...R, G, M and A) must share the same set of column names, because all relate to the same set of arrays. When reading ImaGene data there isn't an...obvious choice of array name, so…

updated 19.7 years ago • Gordon Smyth

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 validation...and Clinical validation. Individual scientists and clinicians work together in groups mostly based on tumour type. The newly created

SNP Sequencing Genetics Cancer Breast SNP Sequencing Genetics Cancer Breast

updated 15.6 years ago • Audrey Kauffmann

to which these genes belong. I have an excel or CSV file with a table with a list of genes, the name of each gene and its GOs number. I do not have statistical information on each gene, how can I find the main processes/GO...common genes are genes that in transcriptome analysis, have increased or decreased their expression levels and I compared the genes between two samples (each time only what …

GeneSetEnrichment genes genetogo

updated 3.5 years ago • Noy

pm(affybatch) gives a single probe value in each row and adds a numerical suffix to the gene name so that each probe has a unique gene name. Instead, I'd like to extract the pm probes into a matrix that has a single Affy gene...name for a row header and the signal values for all of the pm probes for that gene in the following columns of that row. Some genes...with the ratio of that probe signal…

probe affy probe affy

updated 20.9 years ago • Stuart Brown

across samples. I am running into an error with DESeqDataSetFromMatrix which indicates my variable names and column names are not matching When I investigate this I find that they are matching. Any ideas? > head(sample_info_tab...Error in DESeqDataSet(se, design = design, ignoreRank) : all variables in design formula must be columns in colData However when I check that t…

deseq2 normalization

updated 5.6 years ago • ericmalekos

0%Error in quantile.default(M, c(1, 5)/6, names = FALSE) : missing values and NaN's not allowed if 'na.rm' is FALSE</pre> I tried to search where the `` genotype.Illumina `` function

crlmm

updated 8.5 years ago • komal.rathi

matrix of counts. The resulting matrix has 25221 rows and I'm wondering how I can retrieve the gene names for each row.  source("https://bioconductor.org/biocLite.R") biocLite("TxDb.Hsapiens.UCSC.hg38.knownGene") library

rnaseq summarizeoverlaps count matrix

updated 7.8 years ago • johnsonn573

exonHits p "ct_exonHitsm_7841" "ct_exonHitsp_7844" I can use these odd, modified track names, and display the desired: view <- browserView (session, range.to.view, full='exonHits m', dense='ruler', hide=trackNames (session

trigger trigger

updated 15.1 years ago • Paul Shannon

Hi, I’m working with an RNAseq study design similar to the multi-level experiment example from section 9.7 of the limma user guide. I have a 2-level factor called “Genotype” and a factor called...nested within Genotype (3 families of Genotype “F” and 2 families of Genotype “O”). I also have a 2-level factor called “Treatment.” I’m mainly interested in testing the effects of Treatment within the …

limma multiple factor design

updated 10.4 years ago • csmall

Hi everyone! I am studying at the transcriptional level how our cell line behaves when subjected to a certain treatment. I am mainly interested in short treatment times and...come from different studies? (for example, all those on day 2) 2. If my approach is considered valid, what criteria should I use to select the relevant pathways if in some cases they are not all in agreement at the various

meta-analysis DifferentialExpression RNASeq timecourse Pathways

updated 7 months ago • enee

50000-gene Affymetrix, 15 > cancered people and 10 normal people). 40 genes' RNA expressional levels > were found significantly different between the two groups (by two sample > t tests, p values corrected). We are now...planning a second-stage > experiment to validate this finding. We want to do power analysis and > sample size calculation, especially want to k…

updated 19.9 years ago • Kort, Eric

I am working on a more complex design, but I think a basic 2-factor (each with two levels) captures the spirit of my question. Namely, I am interested in creating "reasonable" mock data to appropriately test...analysis. My hypothetical setup takes 2 factors (genetic background and treatment) at two levels each: - `background` factor has levels: sgCtrl, sgFoo - `treatment` factor has lev…

deseq2 deseq

updated 5.7 years ago • blawney

organism so I pulled annotation information from NCBI's gtf file, which has the symbols in a column named "gene". This turns out to cause some internal problem in `glimmaMA()` that tries to put the rownames into a column named "gene...efit <- eBayes(vfit) #This works: glimmaMA(efit, dge = dge) #Change SYMBOL column name to "gene" names(dge$genes)[2] <- "gene" names(efit$g…

Glimma

updated 4.5 years ago • Jenny Drnevich

structure_exon_chrom_end, structure_exon_rank Please use the function 'listAttributes' to get valid attribute names Amanda Miotto a.miotto at griffith.edu.au Software Engineer. Research Computing Services INFORMATION

GenomeGraphs GenomeGraphs

updated 17.3 years ago • Amanda Miotto

kiev.biotech.kth.se> >From: Gordon Smyth <smyth@wehi.edu.au> >Subject: Re: [BioC] Different levels of replicates and how to create a > correct targets file out of that. >Cc: bioconductor@stat.math.ethz.ch > >Dear...not the difference between the patients. The problem is >>how to deal with different levels of replicates and how to …

limma limma

updated 21.6 years ago • Johan Lindberg

Hello all, I am trying to analyze a plant metabolomics database with PAPi, but haven't been able to get even started as there is a constant error apparently related with the data formatting. All examples from the package work fine, and my own data looks in the same format as the example metabolomics data set. My database contains 20 compounds (rows) and 80 samples (columns), the column names are…

papi metabolomics pathway analysis

updated 8.8 years ago • hp71727

DESeq2) Time = rep(c("0h", "120h", "240h"), each = 2) Treat = c(rep("Control", 2), rep("Treat", 4)) nameD <- paste(Treat, Time, c(rep(LETTERS\[1:2\], 1), rep(LETTERS\[3:4\], 2)), sep = "\_") sampleInfo <- data.frame(row.names = nameD, Time = Time, Treat...more variables or interaction terms in the design formula are linear combinations of the others and must be removed

deseq2

updated 7.5 years ago • dryellaboina

mentioned that this is impossible without demanding expression in every sample, because filtering must me done unsupervised (= without knowledge of which condition is applied to each sample), before feeding the data to

edgeR RNAseq DE analysis gene filtering

updated 9.3 years ago • Mau

about the project, see [lab info][1]. **Qualifications:** ------------------- Applicants must have a Ph.D. in bioinformatics, computational biology, statistics, human genetics or related field, and a sound understanding...of biology, data science and statistical modeling. Must be proficient in statistical and programming languages such as R and Python, and familiar with Linux and high perfo…

Bioinformatics RNA-seq Postdoc Genomics Statistical model Job

updated 6.9 years ago • djawaheer

pre> aws ec2 copy-image --source-image-id ami-abd0b3bc --source-region us-east-1 --region us-west-1 --name "Bioconductor 3.3" An error occurred (InvalidRequest) when calling the CopyImage operation: You do not have permission...docs.aws.amazon.com/AWSEC2/latest/UserGuide/CopyingAMIs.html): <pre> The owner of the account must grant read permissions on the storage that backs the AMI,…

amazon cloud

updated 9.1 years ago • Thomas Sandmann

Avenue, Boston MA 02115, rm 536. Persons not already subscribed to the BiocBUG mailing list must register with me to attend the meeting. Just e-mail me with the names of all attendees you are registering. There will be...in Infectious Disease of Military Importance. =============== To access the Channing Lab, you must use Palace Road (parallel to Huntington Ave, just past the Mass College of A…

Microarray GUI Microarray GUI

updated 22.0 years ago • Vincent J. Carey, Jr.

<div class="preformatted">Hi All I am trying to analyze some mRNA illumina bead level data through bead array. Based on the detection p-values(plot attached): if I read it right significant # probes have no expression...div class="preformatted">Hi All I am trying to analyze some mRNA illumina bead level data through bead array. Based on the detection p-values(plot attached): if I read …

probe probe

updated 11.9 years ago • Abhishek Pratap