Bioconductor Forum

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 select certain...probe sets will be ignored for the entire analysis. The difficulty is that there is no consistent naming feature across all probe sets so the only way to identify pr…

Normalization Cancer probe affy PROcess Normalization Cancer probe affy PROcess

updated 8.8 years ago • Schwartz, Donald

version that I am using is 2.15.0 The input for the function was eset and for the intgroup argument character vector "Tissue". There is a column named Tissue in my phenoData of the eset. But it still gives me an error saying the...elements of intgroup do not match the column names of the pData(eset). I don't know what wrong I am doing. The error look like this : Error in prepData(expressionse…

updated 13.5 years ago • Guest User

dataset as predictor variables and Activity as the resposne variable, I would like to do a support vector regression using both linear and non-linear kernels. In my case, I would like to find which of the predictors (out of the...cost: 1 gamma: 0.04347826 epsilon: 0.1 Number of Support Vectors: 66 How to determine now which are the best predictors (out of the 20)…

Classification Regression Classification Regression

updated 11.8 years ago • Guest User

Best regards, Samuel On 17-02-2015 22:55, Mike wrote: it is currently returning a list of named character vectors, it is trivial to convert them to lists simply by, <pre> lapply(files, function(file)as.list(read.FCSheader

flowcore

updated 10.9 years ago • Jiang, Mike

packages and got problems running TCGAanalyze_DEA of TCGAbiolinks with the following error "Error in names(x) <- value : 'names' attribute [7] must be the same length as the vector [5]". No error was reported till the TCGAanalyze_DEA functions

software error

updated 6.2 years ago • messimess

under R 1.9.0 and Bioconductor v1.4: ?Error in boxplot.default(yy ~ xx, xlab = "PrintTip", ylab = "M", names = c("(1,1)", : names attribute [16] must be the same length as the vector [1]? The exact same test code works fine under R 1.8.1 (? and whatever

updated 21.6 years ago • White, Charles E WRAIR-Wash DC

m.4374.path2.0 1A_I11_NT_comp46081_c0_seq2|m.4378.path1.0 rowRanges metadata column names(0): colnames(16): A-P56-1 A-P56-3 ... B-P67-4 D-P56-4 colData names(2): TREAT LAT</pre> 3) when I try to run DEseq(dds) I got this error; <pre> estimating...estimates Error in model.matrix.formula(design(object), data = colData(object)) : data must be a data.frame</pre> 4) I chec…

deseq2

updated 5.4 years ago • mdelrgg

ifnotfound=NA)) This is the error: "Error in .checkKeysAreWellFormed(keys) : keys must be supplied in a character vector with no NAs" Here is the session info: R version 2.15.2 (2012-10-26) Platform: i386-w64-mingw32

illuminaHumanv2 illuminaHumanv2

updated 13.0 years ago • Gaye SAGINC GIS

org.Hs.eg.db', details: call: match.arg(synchronous, c("off", "normal", "full")) error: 'arg' must be NULL or a character vector In addition: Warning messages: 1: package 'oneChannelGUI' was built under R version 3.0.3 2

microarray software error bioconductor

updated 10.2 years ago • o.j.james

Dear Matthew (or anyone that can help me), I am trying to create my own vectors using frmaTools. Therefore I am also using a custom cdf enviroment. But somehow I receive error's trying to create...Dear Matthew (or anyone that can help me), I am trying to create my own vectors using frmaTools. Therefore I am also using a custom cdf enviroment. But somehow I receive error's trying to create the..…

affymetrix microarrays frmatools altcdfenvs

updated 7.8 years ago • osieman52

I have a dds object with these coldata: > head(colData(dds_RNA)) DataFrame with 6 rows and 9 columns Sample Subject Batch Generation Genotype Area Sex Group sizeFactor <character> <character> <factor> <numeric> <character> <character> <factor> <factor> <numeric> 2B2 …

DESeq2

updated 3.6 years ago • A.J.

rma.output,gps=list(1:3,4:6)) But I am not sure what to put for 'ids'. The help package says ids is "Character vector of Ensembl gene names" but I am not exactly sure what that is, or where I get/make that vector. So, I am not able to

probe probe

updated 11.8 years ago • Guest User

quality assessment. In order to do that, I've created a SpotTypes.txt file: <pre> SpotType ID Name Color ncRNA * * black Blank *Blank* * pink PosControl *hsa* * blue NegControl *Randomer* * red</pre> loaded it through readSpotTypes...for: Error in matrix(unlist(value, recursive = FALSE, use.names = FALSE), nrow = nr, : 'data'…

limma custom stf

updated 10.3 years ago • dario.veneziano

produce this error: <pre> Error in `colnames<-`(`*tmp*`, value = c("Chr", "Start", "End", "Conc", : 'names' attribute [9] must be the same length as the vector [7]</pre>   Furthermore, the same samples are (as you see in my contrast

diffbind

updated 8.7 years ago • j.bergenstrahle

in switch(cur$what, environment = cdfFromEnvironment(cdfname, cur$where, : switch: EXPR must return a length 1 vector AffyBatch object size of arrays=712x712 features (3964 kb) cdf=scrMalariaa (??? affyids) number of...in switch(cur$what, environment = cdfFromEnvironment(cdfname, cur$where, : switch: EXPR must return a length 1 vector In addition: Warning message: missing cdf en…

cdf cdf

updated 21.5 years ago • Lana Schaffer

if anybody can say me according to the range of my data, what do I choose for scales and plotRange vectors, so I can see the peaks of the diagram. Thank you in advance &nbsp

MassSpecWavelet Peak Finding

updated 11.2 years ago • s.kazemi.n

directly but got no response from him. My qualm lies with the writing and re- reading of factor vectors using rhdf5. In the current release they are simply written as integers and upon reading the HDF5 files the levels...are obviously forgotten. Of course, I could convert the factors to character vectors before writing but I wanted to ask whether there is a plan to implement better factor suppor…

rhdf5 convert rhdf5 convert

updated 12.9 years ago • Moritz E. Beber

<div class="preformatted">Hi all, I'm running a script that try to normalise 448 HGU133A Affymetrix arrays, and I have "The Error" during the ReadAffy(): Error: cannot allocate vector of size 1770343 Kb I know about R and OSs adressing limitations, so (according to several posts on the mailing list) I'm...HGU133A Affymetrix arrays, and I have "The Error" during the ReadAffy(): Error…

hgu133a hgu133a

updated 18.9 years ago • Ivan Porro

div class="preformatted">Hello everyone. How are you all doing? My name is Desiree. I'm a 1st grad student experiencing problems reading 27 CEL files into R using the ReadAffy command. The total...But after I run the last command, I get the following error message: Error: cannot allocate vector of size 279.1 Mb In addition: Warning messages: 1: In `rownames<-`(`*tmp*`, value = c("1", "…

updated 13.7 years ago • Desiree Wilson

http://", listenAddr, ":", listenPort, appList[[i]]$path, : cannot coerce type 'closure' to vector of type 'character'</pre> Any help will be much appreciated. Below are additional info on my setting.   Here is the output...listenAddr, ":", listenPort, appList[[i]]$path, sep = "") 4: full_url(which(appName == names(appList))) 3: browseURL(full_url(which(appName =…

gCMAP gCMAPWeb

updated 10.6 years ago • afshinmh

details:   call: match.arg(synchronous, c("off", "normal", "full"))   error: 'arg' must be NULL or a character vector Error: loading failed Ejecución interrumpida ERROR: loading failed \* removing ‘/home/clara...details:   call: match.arg(synchronous, c("off", "normal", "full"))   error: 'arg' must be NULL or a character vector Error:…

software error affy microarray

updated 9.3 years ago • superfly7cmz

x' in selecting a method for function 'unlist': Error in .checkKeysAreWellFormed(keys) : keys must be supplied in a character vector with no NAs I also tried your example from the web site ( http://research-pub.gene.com/ReportingTools...x' in selecting a method for function 'unlist': Error in .checkKeysAreWellFormed(keys) : keys must be supplied in a character vector with no NAs So I guess …

Annotation GO Annotation GO

updated 11.1 years ago • Assa Yeroslaviz

the <span style="line-height:1.6; white-space:pre-wrap">vertex.color parameter is a color vector, but it seems that it needs a vector with length is less than my vertex number. </span> For example; <pre> <strong><em>gg<-make_ring

netowrk visualization

updated 7.4 years ago • Wojeff

expression results and I would like to generate a heatmap with each gene plotted in the order of a vector (specifically a biological parameter that all the genes co vary with). I've been wrestling with this for a couple of days...z_mat is my matrix - samples in columns and genes in rows. max_resp is my biological parameter - a vector of values (1 for each subject). What I'd like is a gradient o…

updated 17.3 years ago • Iain Gallagher

missingness when using admixmmap function from Genesis. Column `rsids` joining factor and character vector, coercing into character vector Reading in Phenotype and Covariate Data... Fitting Model with 7485 Samples

genesis admixmap

updated 6.3 years ago • GENOMIC_region

Course Eects of Corn Oil on Rat Thymus with Agilent 4x44K Arrays". I downloaded the same data as named in the package. I tried the following code <pre> SDRF <- read.delim("EGEOD-33005.sdrf.txt",check.names=FALSE,stringsAsFactors...an error. <pre> fit <- lmFit(y0,design) Error in array(x, c(length(x), 1L), if (!is.null(names(x))) list(names(x), : 'data' must b…

limma r

updated 9.5 years ago • Agaz Hussain Wani

sex) <span style="background-color:Yellow"><strong>Error in seq_len(length(idx) - 1) : argument must be coercible to non-negative integer </strong></span>In addition: Warning message: In DESeqDataSet(se, design = design, ignoreRank...exon_name <Rle> <IRanges> <Rle> | <integer> <cha…

DESeqDataSet DESeqDataSetFromMatrix rnaseq deseq2

updated 9.5 years ago • ErickF

Locating AromaCellSequenceFile...done 20121126 20:48:51| Locating...done AromaCellSequenceFile: Name: Hs_PromPR_v02 Tags: Full name: Hs_PromPR_v02 Pathname: annotationData/chipTypes/Hs_PromPR_v02/Hs_PromPR_v02.acs...Located file: annotationData/chipTypes/Hs_PromPR_v02/Hs_PromPR_v02.acm AromaCellMatchScoreFile: Name: Hs_PromPR_v02 Tags: Full name: Hs_PromPR_v02 Path…

Annotation cdf Annotation cdf

updated 13.1 years ago • 周在威

dge <- estimateDisp(dge, design) Error in .compressWeights(y, weights) : weights must be finite positive values</pre>   As you can se no weight is out the rang 0-1 or infinite. <pre> > sum(is.infinite(dge$weights

edger estimatedispersions

updated 7.5 years ago • nonCodingGene

for seqnames only, and doesn't look in mseqnames. It seems like a lot of users of the MEDIPS package must encounter this problem, because most genomes have sets of unassembled scaffolds that, following the BSgenome forging...I do this, the literal BSgenome.Ptrichocarpa.Phytozome.v3 is assigned to the BSgenome variable as a character vector. So instead, I do this: BSgenome = BSgenome.Ptrichocarpa.…

GO BSgenome BSgenome Rsamtools genomes MEDIPS GO BSgenome BSgenome Rsamtools genomes

updated 11.8 years ago • Vining, Kelly

div class="preformatted">Hi Is it possible to filter ranges by imposing condition on name field. I am using the IRanges vignette example below: Require(IRanges) ir1 <- IRanges(start = 1:10, width = 10:1) ir2 <- IRanges...34, 40), width = c(12, 6, 6, 15, 6, 2, 7)) values <- rnorm(length(ir)) rd <- RangedData(ir, name = letters[seq_len(length(ir))], values) rd 1&a…

IRanges IRanges

updated 14.8 years ago • Fahim Md

s13059-018-1406-4][1]). In DESeq2, we can specify contrasts among other things either by a *character vector* (e.g., `contrast = c("condition","B","A")`) or by a *numeric vector* with one element for each element in `resultsNames(object...some elements are recomputed. My issue is that I am getting different results whether I use the character vector or the numeric vector, even if specifying…

zinbwave DESeq2

updated 5 months ago • Aurélie

client", directory = "./Data"). , and I found the following error : “Error: Results must have the same dimensions” Please advice. Thank you

TCGAbiolinks GDC dataset

updated 6.0 years ago • ph.shimaasherif

FILTER AC AF AN BaseQRankSum DP <rle> <iranges> <rle> | <character> <character> <numeric> <character> <list> <list> <integer> <numeric> <integer> 1:3026194_C/A 1 3026194 * | C A 72.28 . 2 1 2 <na> …

vcf snv gatk customprodb inputvcf

updated 6.5 years ago • Elena.M

I have a Run length encoded vector representing some value at every position on the genome, in order. As a toy example suppose I had just one chromosome...of length 10, then I would have a vector looking like library(GenomicRanges) set.seed(1) toyData = Rle(sample(1:3,10,replace=TRUE)) I would like to coerce this into

Rle granges iranges

updated 9.2 years ago • my4

stat.math.ethz.ch > >Hi list, > >I am trying to call makeContrasts() in limma to accept character vector >of all samples vs control. But it seems that makeContrasts() consider >only the first element in the contrast...vector. > >Basically what I've done is first to assign design matrix "dMatrix", >then make a contrast character vector…

limma ASSIGN limma ASSIGN

updated 18.2 years ago • Gordon Smyth

must be issued with dbExecute() or dbSendStatement() instead of dbGetQuery() or dbSendQuery(). 4: In result_fetch(res@ptr, n = n) : SQL statements...must be issued with dbExecute() or dbSendStatement() instead of dbGetQuery() or dbSendQuery(). 5: In result_fetch(res@ptr, n = n) : SQL statements...must be issued with dbExecute() or dbSendStatement() instead of dbGetQuery() …

makeOrgPackage

updated 4.9 years ago • Eduardo Andres-Leon

for mydata' has been created. Error in svgStyleAttributes(style) : All SVG style attribute values must have length 1</pre> and when running a second time <pre> Error in gridsvg(name = "arrayQualityMetrics report for mydata/pca.svg...is as follows: <pre> 7: stop("Only one 'gridsvg' device may be used at a time") 6: gridsvg(name = "arrayQualityMetrics report for mydata/pca.…

arrayqualitymetrics svg software error

updated 9.5 years ago • Paulo Nuin

the sample CEL files using frma and the custom vector featureset <- oligo::read.celfiles(filenames=celfiles.fp, pkgname="pd.hugene.1.0.st.v1") newnorm <- frma(featureset...group length is 0 but data length > 0 I think the issue stems from the fact that the custom vector I create using makeVectorsFeatureSet does not include the "probeVecCore" slot like the pre-built vec…

frma frmatools affymetrix microarrays

updated 9.8 years ago • jperezrogers

matrix of the type <pre> [A] [B] [C] [1] 3 5 2 [2] 1 3 6 [3] 1 6 2</pre> and a vector in the form <pre> [A] [B] [C] [1] 2 4 7</pre> What I am trying to get out is in this case 3 new columns attached to the initial matrix which...would lets say go through all rows in column A and compare it to the value for \[A\] in the vector. If its higher …

matrix

updated 10.3 years ago • BenAbflack

principles behind this package. In statistical modeling and hypothesis testing, a contrast vector c is used to construct specific linear combinations in order to test whether this linear combination equals a certain...condition with four group, to avoid dummy trap & not full rank of matrix, a regression equation must like : Y = Beta_0 + Beta_1 * X_1 + Beta_2 * X_2 + Beta_3 * X_3 + err…

Regression DESeq2

updated 18 months ago • David W. H.

score phase gene_id transcript_id exon_number <numeric> <integer> <character> <character> <numeric> [1] <na> <na> ATMG00010 ATMG00010.1 1 [2] <na> 0 ATMG00010 ATMG00010.1 1 [3] <na> 0 ATMG00010 ATMG00010.1 1...AT1G81020.1 …

GenomicRanges DESeq2 GenomicRanges DESeq2

updated 12.6 years ago • Sam McInturf

<div class="preformatted">I am trying to transform the vector (pm and mm) extracted from @exprs to a matrix (2-D layout), so an image can be plotted. It works out. Now, when I back-transform the...div class="preformatted">I am trying to transform the vector (pm and mm) extracted from @exprs to a matrix (2-D layout), so an image can be plotted. It works out. Now, when I back-transform..…

updated 19.9 years ago • Simon Lin

gio 02/07/2009 8.11 A: Miichael Watson; Sean Davis; Steve Lianoglou Oggetto: Help with symbol names mapping between miRecords and BioMart I extracted some VALIDATED miRNAs and *hopefully* I paired them with their respective...genes 3utr sequence. I am NOT sure about my mapping between BioMart and miRecords objects name. Clearly the output of my algorithm depends upon the correct (is it ?) …

GO Homo sapiens biomaRt GO Homo sapiens biomaRt

updated 16.5 years ago • mauede@alice.it

longest = TRUE ) queryfiles <- c("IP_Aligned.sortedByCoord.out.bam") names(queryfiles) <- c("IP_bam") inputfiles <- c("Input_Aligned.sortedByCoord.out.bam") names(inputfiles) <- c("Input") bamimportParams...0, nc = 2 ) ##error what I got [set_seqinfo] [set_seqinfo] Error in as.vector(x, "character") : cannot coerce type 'closure' to vector of…

GenomicPlot

updated 15 months ago • Lucky

<div class="preformatted">Hello List, I am confused about how to loop over a rangedData object. I have this rangedData RangedData with 61 rows and 1 value column across 3 spaces space ranges | score <character> <iranges> | <numeric> 1 SCAFFOLD_1 [ 8, 8] | -0.09405 and the spaces are "SCAFFOLD_1" "SCAFFOLD_10" "SCAFFOLD_100" using aggregate …

updated 15.7 years ago • Yvan

Hi,  I am trying to color genes in a GeneRegionTrack according to a pre-defined criteria. I have set up the color that I'd like the genes to be in a column of the GRanges object. If I plot the entire GRanges object, then everything works fine. However, if I plot only a portion, then the colors remain in the same order, but they are now attached to different genes. I suspect that this i…

color GeneRegionTrack

updated 9.5 years ago • senanu.pearson

1] file.exists(macs.peaks.file) || stop("macs.peaks.file must exist") result.file <- sub("_peaks.xls", "_peaks_annot.xls", macs.peaks.file) ############################################################## ################## ############################################################## ################## # import peaks peaks.bed <- rea…

GO AnnotationData annotate convert ChIPpeakAnno GO AnnotationData annotate convert

updated 13.8 years ago • Mark Cowley

I am trying to use the topGO package but I get this error message "Error in .local(.Object, ...) : allGenes must be a named vector" when I execute the following command. ``` # Data preparation of reference dataset selGenes <- genefilter(fitted, filterfun(pOverA(0.20, log2(100)), function(x) (IQR(x) > 0.25))) eSet <- fitted[selGenes, ] AllNames <- rownames(eSet) head(A…

Ensembl ensembldb

updated 5.1 years ago • H. Stotz

to run the pam algorithm for k-means clustering, but keep getting the error "Error: cannot allocate vector of size 1048384 K" Any help on how to fix this would be greatly appreciated. Cheers, Dennis </div

Clustering Clustering

updated 19.5 years ago • Wall, Dennis Paul

<div class="preformatted">Hi list. I am having problems with carrying out quantitative analysis with samr. I am trying to correalte gene expression across a microarray data set with weight loss. My expression data is in the form of a matrix and my weight loss data is in the form of a vector. Toy examples (but real data) follow. #expression data wld2 V1 V2 V3 V4 V5 [1,] 7.90 7.5…

updated 17.7 years ago • Iain Gallagher

<div class="preformatted"> can not coerce "CompressedIntegerList" to vector or integer #==================================== ranges <- IRanges(c(1,2,3),c(4,5,6)) filter <- c(1L, 0L, 1L) score <- c(10L, 2L, NA) range2 <- IRanges(start=c(15,45,20,1), end=c(15...div class="preformatted"> can not coerce "CompressedIntegerList" to vector or integer #=============…

updated 16.3 years ago • li lilingdu

div class="preformatted">An embedded and charset-unspecified text was scrubbed... Name: not available Url: https://stat.ethz.ch/pipermail/bioconductor/attachments/20060607/ 3a9bd8ba/attachment.pl</div

updated 19.6 years ago • Darren Ames

contrast``` or ```coef``` parameters with this function. ```contrast``` can receive a list of 2 character vectors, while ```coef``` can receive only elements of ```resultsNames(dds)```. This is issue for me because with ```contrast``` switch

DESeq2

updated 4.4 years ago • יהב

<div class="preformatted">Today I believe I successfuly built a annotation package for my Affy Rat Gene ST data using annotationDbi, at least I got no errors during the build and it loads properly. I get the following error output, however, when I try to run hyperGTest, package Category, on a vector of Entrez Gene IDs and a vector of the gene universe of the chip. I suspect I did something …

Annotation Category AnnotationDbi Annotation Category AnnotationDbi

updated 17.2 years ago • Mark W Kimpel

Similar as this question:** https://stats.stackexchange.com/questions/2592/how-to-project-a-new-vector-onto-pca-space Simple question. How would we project a new vector onto PCA space using **snpgdsPCA( )**, given that there is

SNPRelate

updated 3.8 years ago • MatthaeusCaesar

chr1","chr2")) x RangedData with 2 rows and 0 value columns across 2 spaces space ranges | <character> <iranges> | 1 chr1 [1, 5] | 2 chr2 [6, 10] | y <- RangedData(IRanges(start=8, end=10), space="chr2") y RangedData with 1 row and 0 value columns...across 1 space space ranges | <character> <iranges&…

IRanges IRanges

updated 15.7 years ago • Robert Castelo

and I have a very simple and stupid question, but I couldn undertand how to do that. I have a vector with a column with negative numbers(double). I want to change all negative to positive. I then made a function: ----------------------------- function

updated 12.8 years ago • Guest User

first. No matter what I do, I get the following error message: when the supplied 'genome' vector is named, the names must match the seqnames As far as I can make sense of this message, it seems that there is some mismatch...found some interesting mismatches: The genome in the VCF file is denoted as "b37" and the sequence names are not 100% compatible with hg19. The lengths of chromosomes 1-…

VariantAnnotation VariantAnnotation VariantAnnotation VariantAnnotation

updated 12.7 years ago • UBodenhofer

end) > targetTrack <-with(targets,GRangesForUCSCGenome("hg18",chrom,targetR anges,strand,name,target)) > subTargetTrack <- targetTrack[1] > browseGenome(subTargetTrack) Error in as.vector(x, "character") : cannot coerce...type 'closure' to vector of type 'character' > traceback() 12: as.character.default(call[[1L]]) 11: as.character(call[[1L]]) 10: call…

rtracklayer rtracklayer

updated 11.8 years ago • Guest User