Bioconductor Forum

messages: Warning messages: 1: In result_fetch(res@ptr, n = n) : SQL statements must be issued with dbExecute() or dbSendStatement() instead of dbGetQuery() or dbSendQuery(). 2: In result_fetch(res@ptr, n = n) : SQL...must be issued with dbExecute() or dbSendStatement() instead of dbGetQuery() or dbSendQuery(). 3: In result_fetch(res@ptr, n = n) : SQL st…

annotation AnnotationForge

updated 5.6 years ago • Marcelo Laia

and basic knowledge of UNIX-like operating systems are necessary. The successful candidate must have an excellent publication record from their PhD research. In addition, she/he must demonstrate ambition to have a...complete publication list, grades of master and PhD, motivation letter, research interests and the names and addresses of three referees as one single PDF file directly to [rolf.zelle…

bioinformatician job job postdoc switzerland Job

updated 9.3 years ago • Robert Ivanek

either PDF or ASCII format and include the following: * Basic information: Title, brief description, name and contact information for each tutor, length of the proposed tutorial. * Audience: Proposals must clearly identify the...available). The only restrictions are that the program be freely available or even open source; it must also be related to Life Science applications. The deadline for …

updated 18.7 years ago • Thorsten Meinl

either PDF or ASCII format and include the following: * Basic information: Title, brief description, name and contact information for each tutor, length of the proposed tutorial. * Audience: Proposals must clearly identify the...available). The only restrictions are that the program be freely available or even open source; it must also be related to Life Science applications. The deadline for …

updated 18.5 years ago • Thorsten Meinl

I noticed two different MA plots when I use different inputs for the contrast argument in the lfcShrinkage() function. Both options worked for me but they produced different plots. Does anyone know why and what the difference entails? I used data from datacamp, so my apologies if someone cannot replicate the issue. I added the code I'm confused about betwen exclamation points. data source: http…

DESeq

updated 2.9 years ago • m-bihie

prior to using the "__publish__" function (below), but the issue is that multiple of my dataset row names become NULL following Ensemble-to-Entrez conversion and that causes error in the downstream "publish" function (I can...conditions) colData(mockRna.dse)$conditions <- factor(colData(mockRna.dse)$conditions, levels=c("control", "case")) colData(test.dse)$conditions <- factor(…

reportingtools publish deseq2

updated 10.7 years ago • noushin.farnoud

tab2, hclustfun = hopach) but it crashes and I get the following.... Searching for main clusters... Level 1 Level 2 Level 3 Level 4 Level 5 Level 6 Level 7 Level 8 Level 9 Level 10 Level 11 Level 12 Level 13 Level 14 Level 15 Identified...37 main clusters in level 3 with MSS = 0.08025142 Running down without collapsing from Level 3 Level 4 Level 5 Error in as.dendrogram(hcr) : no…

Clustering hopach Clustering hopach

updated 19.5 years ago • Ivan Baxter

of how to go about trouble shooting it: #Error in cutree(clust.pway, k = jval) : # elements of 'k' must be between 1 and 5 If I set removeGenes to NULL: for ( i in KEGG.ids ) { temp <- findSynexprs(trim(i), attractor.states) } The code...temp <- temp } } #Error in cutree(clust.pway, k = jval) : # elements of 'k' must be between 1 and 5 -- Sent via the gue…

attract attract

updated 13.2 years ago • Guest User

find that most common sequence patters as {A, B } = > 3 from lines 1,3,5. Pls note that A,C,B must not be considered because C comes in between and line 5 also must not be considered because order of A,B is reversed. In simple

spade spade

updated 13.4 years ago • Guest User

Error in .testForValidKeys(x, keys, keytype, fks) :   None of the keys entered are valid keys for 'REFSEQ'. Please use the keys method to see a listing of valid arguments. https://www.ncbi.nlm.nih.gov/nuccore

annotation

updated 8.1 years ago • Ed Siefker

<div class="preformatted">Hi. I'm working with bioconductor since 2 month and I never had any problems. I used CEL-Files from ATGenExpress and everything was okay. Now I tried to analyse different CEL-Files of yeast. I used different sources ( http://chemogenomics.stanford.edu/supplements/01yfh/files/raw_data/tar _archives/ http://www.brownlab.info/publications/Brown2005/celfiles/index.ht…

Yeast cdf affy Yeast cdf affy

updated 19.8 years ago • Roman Brunnemann

can rerun the analysis using a multi-factor design ddsMF <- dds #change the levels of "cell" levels(ddsMF$cell) levels(ddsMF$cell) <- sub("-.*", "", levels(ddsMF$cell)) levels(ddsMF$cell) #rerun DESeq with "treatment" design...the variable is continuous or an interaction term #then the results can be extracted us…

deseq2 design

updated 5.2 years ago • mhnidhi2-c

your learning set (samples with know >> classes) into training and test set. Look up "cross validation". >> >> Some example of built in cross validation >> * knn.cv() is a leave one out cross-validation of knn() >&gt...svm() in library(e1071) has an argument named 'cross' for cross >> validation >> In p…

Microarray Clustering Category Microarray Clustering Category

updated 21.4 years ago • Kasper Daniel Hansen

DU06_PBMC_RNA_L1.sorted.bam" > > countDF <- data.frame(row.names=names(eByg)) > > countDF data frame with 0 columns and 23710 rows > > dim(countDF) [1] 23710 0 > > for(i in samplespath) { + aligns...Warning messages: 1: In .Seqinfo.mergexy(x, y) : Each of the 2 combined objects has sequence levels not in the other: - in 'x': c…

updated 11.6 years ago • Pankaj Agarwal

Hi, My name is Mahes Muniandy and I am a doctoral student working on twin data. I have gene expression (Affymetrix HGU133 plus...c2","c2","c1","c2","c2","c1")) LG <- paste(Cluster, HeavyLean, sep=".") LG <- factor(LG, levels=c("c1.O","c1.L","c2.O","c2.L","c3.O","c3.L")) design <- model.matrix(~0 + LG) colnames(design) <- levels(LG) dupcor <-…

limma

updated 9.9 years ago • mahes.muniandy

of the experimental condition on the chromosomal genes. I was wondering if it's statistically valid to run DESeq2 on chromosome and plasmids separately or if it's more correct running the differential expression analysis

DESeq2

updated 2.2 years ago • Laura

want to reinvent the wheel, and the conversion tool I have here (XML Spy) bitches about it being non-valid. Greetings Johannes </div

probe probe

updated 22.8 years ago • "Hüsing, Johannes"

I know that this data would be unsuitable for DEXSeq (or DESeq/edgeR), but would it be valid to use limma voom on the data? I don't know what statistical assumptions voom makes. Cheers, Ian Sudbery &nbsp

limma voom rnaseq

updated 9.0 years ago • i.sudbery

Hey, I'm trying to preform a bisulfite alignment using gmapR package. This is my code: ========================= library("gmapR") ggd<-GmapGenomeDirectory(file.path(getwd(),"indices"), create=T) gg<-GmapGenome(file.path(getwd(),"test.fa"), directory=ggd, name="seq", create=T) cmet\_index <- cmetindex(gg) gsnapPar <- GsnapParam(genome=gg, unique\_only=FALSE, subo…

software error gmapr

updated 7.0 years ago • Amer Ghalawinji

<div class="preformatted"> After reading in a GTF file with rtrackler::import(), I have a GRanges object. How can I select the ranges whose gene_id (or transcript_id) match a particular value? > library(rtracklayer) > gtf <- import(system.file("tests", "gtf.gff", package="rtracklayer"), asRangedData=F) I can see the metadata with 'mcols(gtf)', and I can even see the …

updated 12.1 years ago • Guest User

<div class="preformatted"> Dear Gviz developers, We have come across an issue while visualizing chromosome 16 of the human genome hg19 using IdeogramTrack and plotTracks. Plotting chr16 produces the following error: Error in lcS[[as.numeric(j) - 1]] : subscript out of bounds while this does not happen with other chromosomes. Please see the minimal example attached below. ##### beginnin…

Genetics Gviz Genetics Gviz

updated 12.6 years ago • Guest User

stringdist The argument of a replacement function which corresponds to the right hand side must be named ‘value’.     The S3 consistency warning does not return a violating function, so I'm not sure what to investigate

cmd check warnings s3

updated 9.3 years ago • anthonycolombo60

in data analysis and programming in a Unix/Linux (preferably with R and Bioconductor) is a must. Knowledge of basic biology is considered an asset. We invite strong candidates holding a PhD in Bioinformatics or PhD...including CV, brief statement of research interests and relevant data analysis experience, names and email addresses of at least 2 referees before November 11th, 2012 by e-mail to …

Sequencing ASSET Sequencing ASSET

updated 13.1 years ago • Mark Robinson

gt; Thanks. I guess this makes sense, but is it possible this way to perform >>> transcript level counting in addition to exonic gene-level counting? >>> >> >> Yes, it can do that. But you will have to provide your...The information in this email is confidential and intended solely for the addressee. >> You must n…

Annotation Rsamtools Rsubread Annotation Rsamtools Rsubread

updated 12.6 years ago • Wei Shi

I have a dataset with 10 condition vs 20 control samples and am using limma to test for differential expression. Broadly, groups are age/sex matched but have added noise due to complex medical histories, which are matched as best as possible but is still far from perfect. Ran through a basic analysis limma pipeline, everything worked as expected. In the same batch, I processed a number of oth…

limma multtest

updated 11 months ago • Ali Barry

a method for function '%in%': Unknown track: rmsk" Listing all available tracks reveals that the name for the track might be: "RepeatMasker". ```r # List all available tracks in the session available_tracks <- trackNames(mySession...print("Available Tracks:") print(sort(available_tracks)) ``` However, when I replace the track name "rmsk" with "RepeatMasker (see below), I still…

UCSC rtracklayer getTable

updated 14 months ago • Andreas.Herbst

timeout In addition: Warning messages: 1: In result_fetch(res@ptr, n = n) : SQL statements must be issued with dbExecute() or dbSendStatement() instead of dbGetQuery() or dbSendQuery(). 2: call dbDisconnect() when finished...working with a connection 3: In result_fetch(res@ptr, n = n) : SQL statements must be issued with dbExecute() or dbSendStatement() instead of dbGetQuery() or dbSen…

AnnotationForge

updated 4.7 years ago • Imad

I have a pair of chipseq. One is really bad. Mapping failed. I was wondering if it's possible to analyse only one without the pair ?  Other question : I tried to do the analyze with both of the samples even is one is not very good. I did two different things : the first time I set the rule that peaks must be in both replicates...that gaves me 1116 differential peaks. <pre> db…

diffbind

updated 8.2 years ago • ZheFrench

Time) > fit = lmFit(data_to_model, design) Error in rowMeans(y$exprs, na.rm = TRUE) : 'x' must be numeric > design = model.matrix(~ fac1 * fac2 * data_to_model$Time * data_to_model$Value) > fit = lmFit(data_to_model, design...Error in rowMeans(y$exprs, na.rm = TRUE) : 'x' must be numeric fac1 is a factor fac2 is a factor data_to_model$Time is a numeric my data_to_model data…

updated 14.4 years ago • Dimitris Kampas

signal around gene, but it gave error like this: Error in intoNbins(gr, bcount) : all 'width(gr)' must be >= 'n'.</pre> My command is : <pre> mg <- metagene$new(genes, "H3K4me3.bam", cores = 8, force_seqlevels = TRUE)</pre> After add the parameter...besides, some times it gave error "</pre> <pre> Error in intoNbins(gr, bcount) : all 'width(gr)…

metagene metagene$new

updated 8.0 years ago • Wojeff

This is my n size: table(metadata_filtered$Fiber_type) #First I created my factor vector with 5 levels corresponding to my 5 groups: vector_factor_fiber_type <- factor(metadata_filtered$Fiber_type, levels = c("Type 1...i = Hybrid_2A_2X-Type_2X, j = Hybrid_1_2A-Hybrid_2A_2X, levels=matrix_design_fiber_type) #Second …

limma Proteomics

updated 3.6 years ago • roger.moreno.justicia

counts in rows. I do not want to use this dataset for DEG analysis, rather I want to find expression levels by TPM. My code is actually working and I'm wondering if it is fine to start with reads mapped to genes instead of transcripts...prior.count=0) VeroTPM <- data.frame(VeroTPM) #Add in the gene names from annotation # Find matching rows based on row names matching_rows <- mat…

GeneExpression GenomicFeatures RNA-Seq TPM

updated 2.2 years ago • gingergeiger22

<div class="preformatted">Dear list I would like to perform mRNA-seq cross-species comparison. In that case it would be necessary to account for the differences in gene length. I already got a reply from the author of DESeq (see below) that this is currently can't be done with DESeq. Is it possible to specify gene-specific normalization factor with edgeR? or to input read counts that have b…

Genetics Normalization Proteome DESeq Genetics Normalization Proteome DESeq

updated 14.3 years ago • mali salmon

recount3") human_projects <- available_projects() #Error: 'recount3_url' is not a valid supported URL since it's missing the URL/ <organism>/homes_index text file or 'recount3_url' is not an existing directory

recount recountWorkflow recount3

updated 3.0 years ago • Max Bone

the following error: Error in flowCore::read.FCS("fusionLMA.fcs") : 'fusionLMA.fcs' is not a valid file I can´t figure out what´s wrong, since the file is an FCS file

FlowSOM

updated 2.1 years ago • agus_rizzo

pkg, character.only = TRUE, logical = TRUE, lib.loc = lib.loc) : 'repeated' is not a valid package -- installed < 2.0.0? I have installed the "arrayCGH" library using getBioC successfully. I cannot find any information

aCGH aCGH aCGH aCGH

updated 21.1 years ago • Christopher, Neil NIH/NCI

marginal tests. FOR instance machine learning methods are based on gene subsets for each of k CROSS validations. USE of the appropriate TEST (fold/T/F/cyber-T/etc..)for subset selection is IMHO the most IMPORTANT!! choice . Stephen

updated 22.0 years ago • Stephen Henderson

ie does human expression match porcine expression?, and reduce the number of probe sets Is it more valid to filter before doing the regression, or after? Thank you -- Loren Engrav, MD Univ Washington Seattle [[alternative HTML

Regression probe maanova Regression probe maanova

updated 16.4 years ago • Loren Engrav

set "`` removeFirstG=TRUE ``",  the error message said "`` Error in checkSlotAssignment(object, name, value) ``". Could this be a bug or my mistake? Thank you! <pre> > i.ce <- CAGEexp( + genomeName = "BSgenome.Bterrestris.bcm.bter1...first base of the reads if 'G' and not aligned to the genome... Error in checkSlotAssignment(object, name, value) : assignmen…

cager

updated 7.2 years ago • Pengcheng Yang

This is my dataset description and what I have done so far: `` Inv Tratamient Day Name 1 1A control 0T EA2SS13.genes.results 2 1A control 0T EA2SS22.genes.results 3 1A control 0T EA2SS31.genes.results...colData(dds) DataFrame with 9 rows and 3 columns Day Tratamient Name …

deseq2

updated 6.8 years ago • Ale

Unable to complete analysis. Warning messages: 1: No contrasts added. There must be at least two sample groups with at least three replicates. 2: No contrasts added. There must be at least two sample groups

ATACSeq

updated 2.7 years ago • Chris

called 'gpllibrary' library(gpllibrary[1]) # Error in library(gpllibrary[1]) : 'package' must be of length 1 library(as.character(gpllibrary)) # Error in library(as.character(gpllibrary)) : # 'package' must be of length

GEOmetadb GEOmetadb

updated 15.4 years ago • Jeremiah H. Savage

to NA. > de.com <- exactTest(d) Error in if (any(dispersion < 0)) stop("dispersion must be non- negative") : missing value where TRUE/FALSE needed > de.com <- exactTest(d,dispersion=0) Error in binomTest(s1[pois...s2[pois], p = n1/(n1 + n2)) : y1 and y2 must be non-negative [[alternative HTML version deleted]] </div

edgeR edgeR

updated 13.4 years ago • Bogdan

mailing-list /posting-guide/ ). As the command you are trying to use is from a deprecated package, namely exonmap, it will likely not be valid in xmapcore (it is not, in fact). You may read the vignettes and reference manual from

exonmap xmapcore exonmap xmapcore

updated 15.1 years ago • Manca Marco PATH

gt; dds <- DESeqDataSet(airway, design = ~cell + dex) Error in checkSlotAssignment(object, name, value) : assignment of an object of class “GRangesList” is not valid for slot ‘rowRanges’ in an object of class “DESeqDataSet

deseq2 genomicranges

updated 8.4 years ago • Levi Waldron

clinically impactful devices, procedures, and biomedical informatics resources; test the clinical validity of those items with likely impact in the personal medicine clinical enterprise; and to execute high priority projects...statement of personal objective and research interests, pdfs of no more than three papers, and the names and email addresses of three references to: Peter J. Tonellato, Ph.…

updated 16.5 years ago • CBMI LPMGEN1

size normalization][2] One way I have thought of to double-check whether the normalization is valid is to check the fragment counts (my data is paired-end) of promoter regions of highly expressed unchanged genes between...bRetrieveAnalysis = T) cnt.table <- counts(dsq.dds, normalized = T) ``` but the row names of the table are just numbers 1, 2, 3, 4, 5... lack of genomic location in…

DiffBind

updated 4.7 years ago • Shuwan

Il10 ko", + annot = annFUN.hgu, + affyLib = affyLib) Error in checkSlotAssignment(object, name, value) : assignment of an object of class "AsIs" is not valid for slot "allGenes" in an object of class "topGOdata"; is(value, "character

GO limma topGO GO limma topGO

updated 18.1 years ago • Caroline Reiff

negative integers what does it mean exactly? maybe that the column range (e.g chr1 1000-1002) must be End - Start > 0? this is my object **ce** > ce A CAGEexp object of 1 listed experiment with a user-defined name and respective...5 metadata(0): assays(2): counts normalizedTpmMatrix rownames: NULL rowData names(3): genes annotati…

CAGEr IRanges aggregateTagClusters

updated 5.6 years ago • mirkocelii

must be issued with dbExecute() or dbSendStatement() instead of dbGetQuery() or dbSendQuery(). 6: In result_fetch(res@ptr, n = n) : SQL statements...must be issued with dbExecute() or dbSendStatement() instead of dbGetQuery() or dbSendQuery(). 9: In result_fetch(res@ptr, n = n) : SQL statements...must be issued with dbExecute() or dbSendStatement() instead of dbGetQuery() or dbSendQuery()…

microarray pdInfoBuilder oligo

updated 5.4 years ago • Marton Papp

Hello all, I am currently performing analysis in R to find whether there are differentially expressed genes between samples with cancer, and without cancer (benign), as a student project. I am using the HuProt array, and thus have around 48,000 observations per sample. Before using limma, I used t.tests to see whether there were any significant genes. This is how I've done the t.tests: ```r p.va…

fdr limmaGUI p-values limma

updated 3.2 years ago • seahorsebox828

<div class="preformatted">Two Research Associates Computational biology / bioinformatics and small RNAs Department of Plant Sciences, University of Cambridge, UK Salary: ?25,134-?32,796 (rising to ?25,888-?33,780 on 1 May 2008) Limit of tenure: funds are available for two years in the first instance Professor Baulcombe?s laboratory is at the forefront of research into small RNAs and th…

Sequencing Sequencing

updated 17.6 years ago • Krys Kelly

lt;- scale(colData$age) # Center and scale the age variable colData$time <- factor(colData$time, levels = c("pre", "post")) # pre as reference colData$condition <- factor(colData$condition, levels = c("Placebo", "Medicine")) # Placebo as reference...samples. Might be bit strigent? dds <- dds[keep,] dds <- DESeq(dds) res <- results(dds, name = "timepost.cond…

DESeq2

updated 6 days ago • Junmo

from a peak list where start is the start of the binding site, end is the end of the binding site, names is the name of the binding site, space is the chromosome name where the binding site is located. If you think having a conversion...3123260, 3857501, 201089), end = c(967754, 2010997, 2496804, 3075969, 3123360, 3857601, 201089), names = c("Site1", "Site2", "Site3", "Site4", "Site5", "Site6…

GO BSgenome BSgenome GO BSgenome BSgenome

updated 16.0 years ago • Julie Zhu

data from GEO148000, [https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE148000][1] The IDAT file names from this project are like GSM4452048_Asthma_9_Grn.idat, GSM4452048_Asthma_9_Red.idat, GSM4452049_COPD_1_Grn.idat...with my file? Do the red and green idat files have to have the Array and slide values in the file names? [1]: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE148000

ChAMP

updated 3.0 years ago • minardsmitha

for top genes rs<-rowSums(de_counts) # Assuming by high count, across all samples top.names <- names( rs[ order( rs, decreasing=TRUE ) ] ) de_counts[top.names, ] # DE genes Ranked ,highest first Thanks, Shreyartha On Wed, Dec 12, 2012...0.05 using the exactTest() function. > Now I need to rank these DE genes based on the expression level (count > values). What is the…

updated 13.0 years ago • Shreyartha Mukherjee

I am running an analysis of transcriptional changes in Drosophila using Affymetrix (Drogene-1_1-st). The issue is that even though I can retrieve the biological annotation for the different probes, I do not know how to then merge the annotation with the primary data. How do I include the biological annotation from "featureData" in the data matrix or the final analysis when I try to identify di…

microarray annotation

updated 6.7 years ago • lm795

Hello, Dr Stark. Recently, I am learning some knowlege about coordinate system of zero based and one based. And It reminds me that I often do some format change in DiffBind :). Just like **1. change the merged coordinate into bed format** ```r dba_meta <- dba(minOverlap = 1, sampleSheet = sample_info) ``` ```r > dba_meta$merged[1:10,] CHR START END 1 1 30…

diffbind Rory Stark coordinate

updated 5.7 years ago • shangguandong1996

<div class="preformatted">Hi, So now I can see a little better what you are doing. The problem is what is happening inside of goProfiles. Now this is not my package and I have never really used it much myself, so I just did a little debugging to see what was happening, and this is what I found: The basicProfile() function is expecting you to give it a central ID for the org package you …

GO Organism goProfiles GO Organism goProfiles

updated 12.3 years ago • Marc Carlson

Hi, I'm trying out the CoSplicEx pipeline that feeds into WGCNA (https://github.com/iancuo/cosplicingNetworks). To test module preservation, the script loads adjacency matrices, but I get an error regarding the rownames. Below, I recreate the error using some random matrices. Any insight into what I may not be specifying correctly would be greatly appreciated! Thanks. ``` > libr…

wgcna

updated 6.6 years ago • maya.kappil