Bioconductor Forum

everyone, I am currently getting information of gene type (eg. miRNA, mRNA, lncRNA) from probes name. For example: 1007\_s\_at for a protein-coding gene (mRNA type), 225799\_at for a long non coding RNA (lncRNA). Can some one

Map

updated 8.4 years ago • landscape95

  I was running a function:       doCimplAnalysis(data = idata, scales = scale, n\_iterations = 1, BSgenome = Hsapiens, system = "SB", verbose = FALSE) However, I encountered a error that I am not sure about: "Error in FUN(X\[\[i\]\], ...) : no slot of name "start" for this object of class "XStringViews"   Called from: FU…

XStringViews biostrings

updated 9.7 years ago • jbtouching

em></pre> 2. In the author's result file before and after annotation, the probeset column has a name "ID".  My result file does not have any name in the first column. Author's file:  <pre> <span style="background-color:Yellow...strong>(storageMode: lockedEnvironment) assayData: 41345 features, 20 samples element names: exprs protocolData rowNam…

limma annotation pd.mogene.2.0.st mogene20sttranscriptcluster.db affy

updated 10.9 years ago • alakatos

c\_\_Clostridia",id="X.SampleID", time="Age", B=10, norm=F, log=F) Error in sort.list(y) : 'x' must be atomic for 'sort.list' Have you called 'sort' on a list? Could someone tell me what is going wrong here? Output of str(pData...obs. of  13 variables:  $ X.SampleID          : Factor w/ 104 levels "C001","C002",..: 54 49 51 …

metagenomeseq fittimeseries

updated 9.2 years ago • wijera81

Good day. I am trying to convert on the chromosome from bam file to GRobject and the to plot with package HilbertCurve. But I receive an error > hc = GenomicHilbertCurve(chr = "chr1", background = reads level = 5, reference = TRUE, Error: unexpected symbol in "hc = GenomicHilbertCurve(chr = "chr1", background = reads level" > reference_gp = gpar(lty = 1, col …

HilbertCurve error bamfiles GRobject

updated 6.2 years ago • adklts

My design consists of one factor i.e. treatment with three levels ``` >dds <- phyloseq_to_deseq2(ps, ~treatment) >levels(dds$treatment) 'Compost''Control''Forest''Groundnut' >dds <- DESeq...My design consists of one factor i.e. treatment with three levels ``` >dds <- phyloseq_to_deseq2(ps, ~treatment) >levels(dds$treatment) 'Com…

deseq2

updated 5.2 years ago • Aditya Bandla

Hi,         I'm doing RNA-Seq data analysis following nature protocol paper (Transcript-level expression analysis of RNA-seq experiments with HISAT, StringTie and Ballgown). But after going to step 10 (bg\_liver\_filt...nbsp;     I'm doing RNA-Seq data analysis following nature protocol paper (Transcript-level expression analysis of RNA-seq e…

genefilter ballgown

updated 7.9 years ago • fubeide

__Job Title: Personalized Medicine Research Fellowship__ Summary:  The Center for Biomedical Informatics (CBMI) at Harvard Medical School has one research fellowship available for immediate appointment. The position is part of the Laboratory for Personalized Medicine (LPM, lpm.hms.harvard.edu), whose focus is to reengineer translational science and accelerate the migration of biomedical…

genomes Job

updated 11.2 years ago • Doe, Aimee

ENSBTAG00000004608 "617660" "407106" NA "100138951" # a named character vector with one NA #now get symbols syms <- unlist(mget(egs, org.Bt.egSYMBOL, ifnotfound=NA)) #throws and error...fair enough - need to drop the NA which(egs == NA) #gives named integer(0) - hmm class(egs) #gives [1] "character" - so I'm quite confused now. NA %in% egs #gives […

Bos taurus biomaRt Bos taurus biomaRt

updated 14.4 years ago • Iain Gallagher

Hi, I have a simple case, design(dds) = ~ sex + batch + condition, where condition is a factor with three levels (A, B, and C). I tried two different ways of testing differential expressed genes between condition B and C: Method 1: Run DEseq...have a simple case, design(dds) = ~ sex + batch + condition, where condition is a factor with three levels (A, B, and C). I tried two different ways of t…

deseq2

updated 7.3 years ago • Xianjun Dong

quantification, and differentially expressed analysis. Could you teach me how to change sample names, e.g. using Chuong533 instead of Users.gary.Documents.Project.20180429\_ZebraFinchColor.20180508\_Analysis.featurecounts.Chuong553.bam

featurecounts edgeR

updated 7.5 years ago • Gary

with the little macro function I wrote to > perform these normalizations. These sorts of name collisions can be nasty. There are, however, some things that package developers can do to make it more difficult for us...pde here=""> users to mess things up. One of them is for more packages to use name spaces. I believe that Eric's helper function would not have confused affy if the aff…

affy affy

updated 20.1 years ago • Seth Falcon

lt;- coldata01$bcr_patient_barcode coldata01$tumor_status <- factor(coldata01$tumor_status, levels = c("with_tumor", "tumor_free", ordered = F)) #(Now, in this level, I stuck in the following codes (codes are in order) coldata01 <- coldata01...ref = "low") #(THE ERROR: Error in relevel.factor(coldata01$tumor_status, ref = "low") : 'ref' must be an existing level) colData(tumo…

DESeq2

updated 4.9 years ago • Pedram

span>_<span style="background-color:Yellow">Error in XXXX (peakAnnoList) :input object should be a named list (see example below).</span> _However, it all works for test files (provided with ChIPseeker) (see example below) Any advice...gt; plotAnnoBar(peakAnnoList) Error in plotAnnoBar(peakAnnoList) : input object should be a named list... > plotDistToTSS(peakAnn…

ChIPseeker named list error plotAnnoBar plotDistToTSS vennplot

updated 7.7 years ago • k.panov

expression analysis. When I get to running DESeq I get an error about "object of class “NULL” is not valid" when I'm creating the aggregated data. running BiocManager::valid() returns [1] TRUE and restarting RStudion didn't solve...filename="master_DE_list.txt", method="union", lfc_filter=TRUE) Error in (function (cl, name, valueClass) : assignment of an object of class “NULL” is not …

DifferentialExpression NanoporeRNASeq DESeq2 GeneExpression DEVis

updated 3.5 years ago • Ana

is the proper procedure to remove these samples from the data? Should I remove these sample file names from the sample sheet, and re-build the RGSet again? Similar question goes to probes identified to have detection p-values...The MSet.swan I got has same dimensions as MSet.raw.reduced, but I don???t know if this method is valid or not. I do know this cannot be applied to get MSet.norm. If this…

Normalization minfi Normalization minfi

updated 12.0 years ago • Guest User

I get the following error message: > as("myArrayLM", def); Error in methodsPackageMetaName("C", name) : 'The name of the object (e.g,. a class or generic function) to find in the meta-data' must be a single string (got an object of class

limma limma

updated 20.2 years ago • Cyrus Harmon

184 / 300  213 / 300  243 / 300  272 / 300  300 / 300 Error in names(res) <- nms :   'names' attribute \[18\] must be the same length as the vector \[1\] Calls: ChIPQC -> bplapply -> bplapply -> bplapply

ChIPQC

updated 8.4 years ago • seasky002002

the DESeq2 pasilla dataset example, but not for my own data, which gives an error: ``` Error in names(ls.mean) <- sapply(nam, paste) : 'names' attribute [2] must be the same length as the vector [0] ``` It's not clear to me where in the vsBoxPlot

vidger

updated 5.5 years ago • bbj23

Error in spia(de = DE\_Colorectal, all = ALL\_Colorectal, organism = "hsa",  :   de must be a vector of log2 fold changes. The names of de should be included in the refference array!   Could you please help! Regards

SPIA

updated 9.4 years ago • saamar.rajput

Error in data.table::fread(input = mutsig, sep = "\t", stringsAsFactors = FALSE, : input= must be a single character string containing a file name, a system command containing at least one space, a URL starting 'http

maftools mutsig

updated 6.8 years ago • rina

different medical specialties Over a dozen sortable fields Listing of American Pharma Companies Names and email addresses of 47,000 employees in high-ranking positions American Hospital List Full data for all the major...Dramatic cost reduction: $393 for all 5 datasets reply by email: Casey at prolistsource.info valid until Sept 26 2009 By emailing exit at prolistsource.info you will …

updated 16.2 years ago • radcliffe

and CD8 lymphocyte populations. However, there appears to be no way to give the second gate a unique name for the workFlow. I use a quadrantGate to create filters for channels PE.Cy7.A and PerCP.Cy5.5.A. The quadrantGates...slightly different for the CD4 and CD8 populations (though that does not matter here). The 'action_' name in the workFlow is different for each one, but the workFlow node nam…

updated 14.1 years ago • Aric Gregson

Hi, my name is Henry Luo. I am NCU master student from Taiwan. I need some help. Recently I do my project about probe design to detect...Hi, my name is Henry Luo. I am NCU master student from Taiwan. I need some help. Recently I do my project about probe design to detect environmental...Hi, my name is Henry Luo. I am NCU master student from Taiwan. I need some help. Recently I do my project about…

probe affy

updated 5.2 years ago • henry1995910343

and case studies. I have searched the internet but found just discussions in which the "statistical level" was too high for me. Would you please give me some code examples to get these lists? The first problem may be the setting...Both Between and Within Subjects)? Thanks in advance to whom will reply and sorry for this "low level" question. Alessandro -- output of sessionInfo(): R version 2.1…

RNASeq edgeR RNASeq edgeR

updated 12.5 years ago • Guest User

anyone explain what is being used to compute different features within computeFeatures? I get the naming convention being applied that is spelled out in ?computeFeatures. I don't understand the .0., .a. and .Ba. labels. For example

ebimage

updated 11.2 years ago • Max Kuhn

which is the test data set. Checking samples table... Populating samples table... Error: Column name mismatch. My environment is Ubuntu 16.04, R 3.4.2, RSQLite 2.0, cummeRbund 2.18.0.          Any one knows

software error

updated 8.0 years ago • zuolin.bai

GeneRegionTrack",chromosome="chr5", genome="hg19", rstart="exonStarts", rends="exonEnds", gene="name", symbol="name2", transcript="name", strand="strand", name="RefSeq Genes", feature="name2", showId=T, from=122428653, to=122432628) &gt...from=122428653, to=122432628) Error in unit(rep(1, n), "strwidth", data = data) : 'x' and 'units' must have length > 0 > traceback() 12: sto…

updated 13.3 years ago • Winston Timp

Hi BioC List from {sunny}San Diego, CA! [Question]: * How do you map KEGG gene IDs to textual gene names, gene descriptions via BioC? For example, I am interested in knowing which genes are involved in the calcium signaling...pathway in rattus norvegicus, so I did: > library(KEGG) > # map pathway id to pathway name > KEGGPATHID2NAME$"04020" [1] "Calcium signaling pathwa…

Rattus norvegicus Rattus norvegicus

updated 17.9 years ago • Elliot Kleiman

Hi, is there any way to extract the whole clustering structure of the all the nodes in the containers created with the command 'nesthc'? I would like to have something like two mapping vectors specifying for each node in the graph the 1st- and 2nd-level on containers in which they are clustered. So if I have a graph with 8 nodes divided in 2 big containers, and each one of the...to hav…

reder graph

updated 8.1 years ago • luca.zoccarato

Hi, I am trying to do comparative RNA-seq analysis with DESeq2. My purposes are: **1. combine transcripts into genes 2. detect gene expression difference under different conditions 3. obtain a summarized gene expression table** 1. combine transcripts into genes I basically followed these commands: https://bioconductor.org/packages/release/bioc/vignettes/tximport/inst/doc/tximport.htm…

deseq2 tximport

updated 6.8 years ago • marie

las=2) Error in sort.int(x, na.last = na.last, decreasing = decreasing, ...) :   'x' must be atomic In addition: Warning messages: 1: In is.na(x) : is.na() applied to non-(list or vector) of type 'S4' 2: In is.na(x) : is.na() applied

affy package boxplot hgu133plus2 oligo package

updated 8.8 years ago • Javier Pérez Florido

Hi, I am trying to convert a list of KEGG pathway name to corresponding KEGG IDs. To do that, I am using KEGG.db, Version 3.1.2. It seems that this package is not complete, for example...nbsp; keggid2name\["04261"\] Do you have any idea about where can I find complete list of pathway names and IDs

KEGG.db KEGG id

updated 10.6 years ago • NS

I am working with a custom Affymetrix 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

probe probe

updated 18.8 years ago • Karin Lagesen

<div class="preformatted">Dear Gordon Smyth, bioconductor list, In the limma package we found a function called, removeBatchEffect, which removes the effects of batch effects or other technical variables on a gene expression matrix. The code of this removeBatchEffect is as follows: function (x, batch, batch2 = NULL, design = matrix(1, ncol(x), 1)) { x <- as.matrix(x) batc…

limma limma

updated 9.4 years ago • Djie Tjwan Thung

I split the Covariate in two Vectors where one Vector contains only the samples with the lowest level of the covariate e.g. CovBase = c(0,0,0,3,0,3,0,0) and where the other vector contains all the samples with higher levels of the

limma limma

updated 12.3 years ago • Moritz Hess

analysis (control vs patient) on such a variable dataset. Is there a way to control for the level of degradation? like design ~degradation+condition ? or should I use surrogate variable analysis to remove unwanted

degradation RNA-seq variability differential expression brain

updated 8.7 years ago • aec

factor(group) design <- model.matrix(~0+group) Contrasts <- makeContrasts(A.x-B.x, levels=design) res <- glmQLFTest(fit, contrast=Contrasts) Contrasts2 <- makeContrasts(A.x-B.y, levels=design) res2 <- glmQLFTest...fit, contrast2=Contrasts2) Contrasts3 <- makeContrasts(A.y-B.x, levels=design) res3 <- glmQLFTest(fit, co…

edgeR DEG RNASeq DESEQ2

updated 3.8 years ago • Raito92

header = TRUE, row.names=1) > genelist_topGO_5d_1d_all <- as.numeric(gene.table$p.value) > names(genelist_topGO_5d_1d_all) <- as.character(row.names(gene.table)) #My geneList looks good, just like the example, e.g...I try this below > genelist_topGO_5d_1d_all_2 <- as.character(gene.table$p.value) > names(genelist_topGO_5d_1d_all_2) <- as.c…

Microarray topGO Microarray topGO

updated 14.1 years ago • oystercow

Hi,   I have been using featureCounts to obtain both exon- and gene-level read counts (reads were aligned with STAR). For one particular gene (ARID5B, which has 12 exons, 5 unique to one isoform, 2...gene-based read count. This is not posssible as featureCounts uses the exon-union method for gene-level counting. Below are the relevant parameter settings for featureCounts: gene-based …

rsubread featurecounts exon mRNAseq

updated 8.5 years ago • inah

design = ~Genotype + Time + Treatment + Genotype:Treatment + Time:Treatment) #check reference levels dds$Genotype #Answer: Levels: ON OFF dds$Time #Answer: T18 T2 T6 dds$Treatment #Answer: DMSO DRUG #Therefore current reference...level is MYC ON, vehicle, 18h. #It would make more sense to me from an experimental flow standpoint if the current reference level...for 2h timepoint - differential ef…

DESeq2

updated 2.3 years ago • james.zhang20

science, the master in computer science engineering and the master in computer science. Bachelor level courses are taught mainly in French, master level courses exclusively in English. ## Research The successful candidate...scientific computing. ## Function - Be responsible for teaching courses at all study levels (i.e. undergraduate and postgraduate), as well as in programmes of…

Jobs

updated 5.1 years ago • Laurent Gatto

<div class="preformatted">Hi, I've just realized that a call to unique on a DNAStringSet would result in the names slot to disappear. There's nothing about this in the documentation, but if that's the desired effect, warning about it would...preformatted">Hi, I've just realized that a call to unique on a DNAStringSet would result in the names slot to disappear. There's nothing about th…

updated 13.4 years ago • Nicolas Delhomme

stat.math.ethz.ch > Subject: [BioC] analysis histone methylation of Arabidopsis at genome level > by ChIP-Chip? > > Dear list members, > > i would like to ask is there any package or software designed for analysis...gt; histone methylation of Arabidopsis at genome level by ChIP-Chip? > any advice will be very appreciated. > > Best. &a…

updated 16.4 years ago • lidaof

outputDir = "." ) # Invalid keytype: GOALL. Please use the keytypes method to see a listing of valid arguments. sessionInfo( ) R version 4.4.0 (2024-04-24) Platform: x86_64-pc-linux-gnu Running under: Ubuntu 22.04.4 LTS Matrix

clusterProfiler makeOrgPackage gseGO

updated 15 months ago • NURIA

Dear Dr. Leek, I am a new user of the SVA package and try to remove the batch effects for our data. Your sample data works well. When I start my own .csv data (name as HBVHCC), the following code showed the errors. Is the code useful for the .csv file? Do you have a code to solve this problem? I appreciate your support. Best Regards, Jing Shen   mod = model.matrix(~as.factor(cancer)…

getting error in gsva function

updated 9.5 years ago • js2182

FALSE, tryRC = FALSE, n = 2000, verbose = TRUE) ``` 0 out of 712 were assigned to the species level. Of which 0 had genera consistent with the input table

Metagenomics dada2 MicrobiomeData

updated 17 months ago • abhisek001

and exploring other people's questions on support sites, I think it is possible to do this in DESeq2, namely to compare two contrasts. In my case, between 3D and 2D within the same genotype, normalized to their respective WT groups...I think it is making. Explicitly, how to make sure the contrast is using the correct reference level (either WT in 3D, or WT in 2D for A in 3D and A in 2D, respectiv…

deseq2

updated 5.1 years ago • Nick F

preformatted">dear all, the Medical University Innsbruck has a open position at full Professor level in bioinformatics. below I've attached the official text: The Biocenter at the Medical University of Innsbruck is inviting...applications for a TENURE-TRACK faculty position at the Full Professor level in Bioinformatics. The position will start July 1, 2009. Candidates should have recognized …

Cancer Cancer

updated 16.9 years ago • Johannes Rainer

and data integration. This position will work closely with the sequencing group. This is NOT a PhD level position, and we prefer someone has BS or MS degree and past experience in programing, Linux environment, and processing

JobPosting

updated 3.3 years ago • zhen-fu

loads two (or more) ExpressionSets from different RData files, checks that they have same row names (to validate that they are from the same type of array), and concatenate them into one larger expression set. I can get everything

updated 14.6 years ago • Richard Leduc

Bioconductor/eg/Aflavus/rnaseq/"), : Your organism has no mapping defined to perform the validity check for the UCSC compliance of the chromosome name. Defined organism's mapping can be listed using the 'knownOrganisms...function. To benefit from the validity check, you can provide a 'chr.map' to your 'easyRNASeq' function call. As you did not do so, 'validity.check' is turned off

Annotation Organism DEGseq easyRNASeq Annotation Organism DEGseq easyRNASeq

updated 12.9 years ago • Guest User

pre> It turned out that I am able to use the function with multiple reference sequence names like this, for example: <pre> bamDataRanges <- getReadCountsFromBAM(BAMFiles, sampleNames=paste("Sample",1:2), <strong>refSeqName...quoted below) suggests that the function is only capable of handing a s…

cn.mops

updated 8.8 years ago • Mohammad Alkhamis

div class="preformatted">Anyone know a simple method to harvest the raw probe set level expression data (not individual PM probe or PM-MM probe pair level data), which will be summarized by average difference...and then export that into excel with the Affy ID or "probe set name" as row headers and columns representing samples? Second question, I have a small affy custom array. I want to selec…

Normalization Cancer probe affy PROcess Normalization Cancer probe affy PROcess

updated 8.7 years ago • Schwartz, Donald

<div class="preformatted">Hi All, I want to analyze golub data set and apply kkn.cv (knn with cross validation) but i keep getting this error (please scroll down, please) library(golubEsets) X <- exprs(golubTrain) X[X < 100] <- 100 X[X 16000] <- 16000 mmfilt <- function(r = 5, d = 500, na.rm = TRUE) { + function(x) { + minval &…

updated 22.2 years ago • Hrishi D

first, whether the linear model is a good fit of the real data. The common check is residual plot to valid the model assumption. However, one residuals from stats package and one residuals.MArrayLM from limma package, basically...from R, from there I knew how to work around to extract residuals from limma model. However, there must be a easy way to exract the residuals from limma linear model. P…

Microarray limma Microarray limma

updated 18.2 years ago • Tiandao Li

1.0 isexpr2 <- apply(y$E > cutoff, 1, function(z){ any(sapply(levels(Treatment), function(treat){ sum(z[Treatment == treat]) >= sum(Treatment == treat)*proportion })) })</pre> For this example, the normal...algorithms, but I am not sure whether this is quite the same …

limma filtering

updated 8.6 years ago • jamie.gearing

my 'fc' object. This is my code (the relevant parts to my problem): fragmented\_Rn6=read.table(file="valid fragments only\_Rn6.tab",header=TRUE)  fragmented\_Rn6$leftSize=as.numeric(fragmented\_Rn6$leftSize) fragmented...__Error in Ops.factor(runValue(e1)\[which1\], runValue(e2)\[which2\]) :    level sets of factors are different__ Does anyone know why? &…

fourcseq

updated 9.4 years ago • tlgolan

Of the 10000, 7000 can be annotated and 6000 have a GO function assinged to them at a suitible level. Say for this example there are 30 Go clasess that appear. I then conduct Fisher's exact test 30 times on each GO category...of terms in the expressed set and correct for multiple testing. My question is on the validity of this procedure. Just from experience many genes will have multiple functio…

GO Category GO Category

updated 21.8 years ago • Nicholas Lewin-Koh

with different age and gender. I would like to know whether these covariate affect gene expression levels. If they do not have any effect remove them from model and create simpler model for differential expression analysis

edger deseq2 model matrix differential expression

updated 9.2 years ago • ta65