Bioconductor Forum

Affymetrix Human Exon 1.0 ST array My goal is to compare RNASeq with Exon array data at the gene-level and exon-level. To be fair, I was suggested to generate RPKM/FPKM value for each gene and exon using the Affymetrix Exon...From Affymetrix website, I selected "Human Exon 1.0ST array", then downloaded the probeset/exon-level annotation file named "HuEx-1_0-st-v2.na32.hg19.probeset.csv". I have…

RNASeq Annotation RNASeq Annotation

updated 11.4 years ago • shirley zhang

the process correctly): when I am exporting the csv file, there are duplicate entries for some gene names (i.e. ESR1). I am under the impression that RMA and the process I am using (target = 'core') summarizes at the gene level, so I am not...some mouse array data (mouse gene 10 st arrays) and have not run into this problem of duplicate gene names. Any insights on what I might be doing incorrec…

Annotation PROcess Annotation PROcess

updated 11.7 years ago • Guest User

<div class="preformatted">Dear List, I am trying to perform a simple pairwise comparison in simpleaffy, which I have done before, but something goes wrong at the first step. > rawP<-read.affy() Error: the following are not valid files: ./'BB52.CEL' ./'BB46.CEL' ./'BB58.CEL' # (complete list of CEL-files in directory) #The covdesc-file is there and looks ok: &gt…

simpleaffy simpleaffy

updated 17.6 years ago • Boel Brynedal

I am trying to apply `rma` from `oligo` package into data of file `GSE22247_non-normalized_data.txt` from this study: [GSE22247][1] Did: # read txt file into dataframe: rawtxt <- read.delim(paste0(txtpath), sep='\t', skip = 4, header = T) # convert dataframe into expression set: rawData <- new("ExpressionFeatureSet", exprs = as.matrix(rawtxt)) # apply r…

oligo biobase GEOquery

updated 6.1 years ago • salamandra

I would like to use the Gviz package but my I have a reference genome in FASTA format, not as a valid UCSC genome (it was not published yet). It is possible to use this FASTA file instead? Updated for @Florian: Let´s say that...I would like to use the Gviz package but my I have a reference genome in FASTA format, not as a valid UCSC genome (it was not published yet). It is po…

gviz UCSC

updated 10.0 years ago • Vinicius Henrique da Silva

div class="preformatted">Dear all, Is it possible to use a string as an environment name in mget? I was trying to do this with the following script, but it says that the second argument for mget is not an environment...genes, envir=env))) Error in mget(x, envir, mode, ifnotfound, inherits) : second argument must be an environment The following works fine: > refseq<-as…

updated 19.0 years ago • Jarno Tuimala

I should use vst and rlog data for cox model in deseq2 analysis, but if I want to use geo data to validate my model, can I directly apply the model to my geo data, or should I scale data both in geo and tcga before build and validate

deseq2 normalization

updated 5.3 years ago • linouhao

div class="preformatted">Dear all, Can I get the leave-one-out cross validation error of randomForest in R? I only found tune(), which got the 10-fold cross validation error. Thanks for any information

updated 20.9 years ago • Liu, Xin

columns(0): sequences(0): rd1 <- RangedData(IRanges(start=1:3, end=4:6, name=letters[1:3])) rd2 <- RangedData(IRanges(start=1:3, end=4:6, name=letters[4:6])) rbind(rd1, rd2) RangedData: 6 ranges by 0 columns columns...6 1 [3, 6] | rd1 <- RangedData(IRanges(star…

IRanges IRanges

updated 15.8 years ago • Robert Castelo

alias > >> entries, and all their arguments documented. > >> The \usage entries must correspond to syntactically valid R code. > >> See the chapter 'Writing R documentation files' in manual 'Writing R &gt

updated 14.7 years ago • Dan Tenenbaum

Condition_res_vs_sen" [3] "Conditionsen.TreatmentCB" "Conditionres.TreatmentCB" > levels(dds$Treatment) [1] "DMSO" "CB" > levels(dds$Condition) [1] "sen" "res" res = resistant sen = sensitive DMSO and CB are a drug treatments...DMSO and sen are the refs *To really specify my confusion it is mainly the results names [3] and [4], but it wou…

deseq2

updated 6.4 years ago • dennism9251

September 20, 2006 10:22 PM To: Justin Borevitz Cc: 'Scott Smemo' Subject: RE: genotyping RLMM probe level model? Oh, ok. Now I see where you are going. As far as I am aware no one is doing that specifically. At one point I was thinking...RMA to summarize probes prior to analysis eg > Classify(). But what about analysis at the probe level? I'm developing some > SNP/tiling arrays, …

SNP probe RLMM SNP probe RLMM

updated 19.2 years ago • Justin Borevitz

I got the following error report: Error in library(exon.pmcdf) : 'exon.pmcdf' is not a valid package -- installed < 2.0.0? Does anybody have an idea what might be causing this problem? Best regards, - Essi Lahti [[alternative

cdf cdf

updated 17.5 years ago • Essi Lahti

Hi all,     have a general question, one that I would really like some help with if somebody would be able to offer some advice. I am using R to analyse my RNA-seq data, however, I work only from the step where the sequences have been aligned and counts generated to form a counts table with ens IDs, so I am not really clued in about the alignment process.  &…

alignment Fastq fasta

updated 7.1 years ago • A

Hi, I am trying to use annotatr with custom annotations from a bed file to annotate differentially methylated regions. the bed has the following columns: chr, start, end, name (enst), score, strand, enst, entrez_ID, gene_name. I have tried a couple of options but did not manage to have the enst, entrez_ID, gene_name in the annotations. Below are my attempts and corresponding errors. Any advi…

annotatr

updated 2.6 years ago • luca.s

0 0 0 0 0   `` I cannot plot  a graph because my row names and column names dont match. `` library(graph) g = as(x4, "graphNEL") plot(g, "neato") Error in asMethod(object) : 'rownames(from)' and ' colnames...from)' must be identical

graph rgraphviz

updated 11.1 years ago • tyrone.williams.701

I am getting this error- "x must be numeric" when running this code. I am working on a pre processed data. The data frame is list. ``` #moderated t test using limma...file <- rma # Column 1 contains row-names group <- rep(0:1, c(3,5)) library (limma) lmFit(object, design=NULL, ndups=1, spacing=1, block=NULL, correlation, weights=NULL, method

limma

updated 3.9 years ago • keervanik

listInputBam, genomeName="hg19")</code> `` Get UCSC ensGene annotations. `` <code>Error in names(trackIds) <- sub("^ ", "", nms[nms != "new"]) :<br/>   'names' attribute [210] must be the same length as the vector [209]<br/> In addition: Warning...genome(session) <- "hg38"</code> <code>> track_names <- trackNames(sessio…

rtracklayer ucsc ensgene

updated 7.6 years ago • chrisamiller

expressed genes for each factor and I was wondering if some of these genes have an expression level in all the arrays near to the background for removing them from my final list (it's an "eyeballometric" method and the cut...off is arbitrary, I know). So, I've been observing the expression levels of some genes in Affy and in GCRMA and I've observed some differences. I expected some differences, b…

affy limma gcrma affy limma gcrma

updated 21.2 years ago • Jordi Altirriba Gutiérrez

I am having trouble getting specific coefficient names after running DESeq2. The coefficients I get when I run resultsNames(dds) are "Treat1", "Treat2", etc instead of "Treat_B_vs_A...code that I was running and the output are below: ```r samples$Treat <- factor(samples$Treat, levels = c("A","B","C","D","E","F")) samples$Treat # A A A B B B C C C D D D E E…

resultsNames DESeq2 coefficient

updated 4.6 years ago • jkhudyakov

read in using methylumIDAT. As this results in a MethylumiSet object, I am wondering whether it is valid to convert this to an RGChannelSet using `methylumi:::methylumiToMinfi` in order to normalise using the `preprocessXXX

normalization minfi methylumi

updated 6.7 years ago • Pem

always gives "Adjusting for optical effect.Error in assayDataElementReplace(object, "exprs", value, validate = FALSE) : unused argument (validate = FALSE)" Does anyone know how to resolve? Thanks, Jianhai

gcrma

updated 8.5 years ago • zhang.jianhai

trouble when trying to make the annotation object. According to the guides, you need to provide a named vector to the `` col `` argument in `` HeatmapAnnotation `` function, however I can't do that when generating dynamically...as there's different annotations. I've tried an un-named vector, but I get the following error every time: <pre> Error in ColorMapping(name = name, color…

complexheatmap

updated 9.3 years ago • andrew.j.skelton73

I'm sorry that this question might be obvious for statistician. The general question: How to validate the normalization outcome? Density plots? I have tried "loees with aquantile" and "vsn" and outcome of the decideTests

Normalization Normalization

updated 20.0 years ago • krasikov@science.uva.nl

R. The first part is not giving any problems, but in the second part I get an error that a uniquely valid column must be specified. It is actually an existing column, so I don't understand why it is not valid. Does anyone have a...by.x="Sample_Name", by.y="row.names", sort = FALSE) Error in fix.by(by.x, x) : 'by' must specify a uniquely valid column

methylationArrayAnalysis ChAMP MethylationArrayData

updated 4.4 years ago • FWNL15

Hi all, I am willing to import RSEM sample.isoforms.results files with tximport and have transcript level information summarized to gene level (Gene Name). The endpoint is to perform differential expression analysis with...I am planning to provide a tx2gene file in which each transcript points to the corresponding Gene Name. Is the code below correct? Please accept my apologies for this basic …

tximport

updated 4.4 years ago • luca.s

preformatted">Dear list, I have gene expression data with probeset IDs & gene set data with gene names. So both gene set and expression data are not using the same gene ID system. Both gene set and expression data should use...is a requirement of the GAGE analysis. So the problem is that if i convert the Probeset IDs to gene name, i get a single gene name for multiple probes. So the ex…

convert gage convert gage

updated 13.7 years ago • Javerjung Sandhu

Any thoughts on what am I missing? Thank you very much in advance. My code is below. ## 1 ## > levels(colData$genetics) [1] "129" "B6" > levels(colData$environment) [1] "black" "yellow" > dds <- DESeqDataSetFromMatrix(countData...genetics:environment) > dds <- DESeq(dds) > resG <- results(dds, alpha=0.05, name="genetics_B6_vs_129") &am…

RNASeq Genetics DESeq2 RNASeq Genetics DESeq2

updated 11.1 years ago • Guest User

I would like to confirm these clusters and to estimate the robustness of this clustering by cross-validation and/or bootstrapping(*). For that, I have two questions: 1) Does there exists an appropriate package and/or source to...perfom cross-validation and/or bootstrapping? 2) Which is the right measure to rate the goodness of such a clustering? By now, I looked over

Clustering Clustering

updated 20.1 years ago • Heike Pospisil

Dear All, I am trying to use Shiny package from R. I have a user typed input and the code behind takes that input runs it across several databases and returns tables.(See the code attached below) What I need is instead of returning empty tables I should print an error message saying that an input is required. I havent accomplished that (tried validate and need) . Please also note that I am not i…

R validate shiny

updated 10.1 years ago • alptaciroglu

matrix. I noticed that on the SNM help page, it highlights the necessity of making the model matrix valid. However, I am not sure how to determine if the model matrices are valid. Could anybody please help? Thank you very much. Wendy...Y = raw.dat, bio.var, adj.var, int.var, spline.dim, : cbind(bio.var,adj.var) is not a valid model matrix. Enter '?model.matrix' for more information on buildin…

snm snm

updated 14.1 years ago • Wendy Qiao

RNA-seq data using DESeq2 pipeline ][1], I have learned that depending on context, it is perfectly valid to remove X and Y chromosomal genes in RNA-seq data before doing differential expression analysis. However I only have...of the RNA seq data I am analysing. Is it advisable to do the X and Y chromosome gene removal at the level of the count matrix? I am talking about removing all rows that con…

deseq2

updated 6.7 years ago • charlesgwellem

1]] %in% lb, "orange", "grey") label_color[is.na(label_color)] <- "grey" names(label_color[label_color == "grey"]) <- "NA" names(label_color[label_color == "organe"]) <- "lysosome

EnhancedVolcano

updated 2.7 years ago • Phương Thùy

<div class="preformatted">Bioinformatics Specialist(Full-Time) Biostatistician To work closely with Ph.D. level biologists in the area of quantitative genetics, including array analysis and software development. Strength in computer...preformatted">Bioinformatics Specialist(Full-Time) Biostatistician To work closely with Ph.D. level biologists in the area of quantitative genetics, in…

Genetics Genetics

updated 22.4 years ago • Joanne Chory

end-start+1; return iranges; }</pre> This is my code so far, it can return GRanges but is not valid for conversion to GRangesList, because columns are wrong types. \#IN R ->: <pre> library(Rcpp) require("IRanges") require("GenomicRanges...start") = 0; ranges.slot("width") = 2; char strand = '+'; //Strand string names = "abc"; //Names of GRanges …

GRanges IRanges RCPP Constructor

updated 8.1 years ago • hauken_heyken

duplicate entries, and NAs. The entrezgene IDs are valid. In fact, I can run the analysis on Graphite's online version of SPIA using the "all\_genes" and "sig\_genes" vectors/files...better graphing options.  I think the problem has something to do with my creation of the named vector __sig\_genes__(below), which contains the log2FoldChange values named with Entrezgene IDs.  I…

SPIA named vectors pathway analysis

updated 11.1 years ago • A Eelmur

When I used ChIPQC, I followed the manuals to construct a sample sheet (name is "examplefile.csv"), and then run: >a <- read.csv("examplefile.csv") >b = aa = ChIPQC(a, annotation=NULL) air\_k14\_2 air\_k14...When I used ChIPQC, I followed the manuals to construct a sample sheet (name is "examplefile.csv"), and then run: >a <- read.csv("examplefile.csv") &am…

software error bioconductor chipseq chipqc

updated 10.3 years ago • wangzhe335

I get an error: "Error in contrasts.fit(fit,contrast.matrix): Number of rows of contrast matrix must match number of coefficients In addition: Warning row names don't match col names of coefficients" for the following Timecourse...Stimulated (LPS) versus Unstimulated (CON) cells Affy Gene1.0 chips The targets are ChipNumber Name Filename Time Treatment Biolrep 1 …

TimeCourse timecourse TimeCourse timecourse

updated 16.8 years ago • David Martino

<div class="preformatted">Hi I downloaded GSE2034 dataset from GEO. But when I tried to read in these cel files using ReadAffy(), I got the following error message: > library(affy) > fls<-list.files("my directory to CEL files", ".*cel")## get cell files > aBatch<-ReadAffy(filenames=fls)## input raw CEL files Error: the following are not valid files: G…

updated 14.5 years ago • array chip

expression") ``` It throws > Error (scratch_11.R#9): Error in h5checktype(). H5Identifier not valid. What should I do as extra step to solve the issue? When I run ***h5ls("archs4_gene_human_v2.1.2.h5")***, the output looks like...this: ``` group name otype dclass dim 0 / data H5I_GROUP …

rhdf5 rhdf r

updated 2.7 years ago • Nargil

col = list(Species = col_vector)) Instead, what I try to do is to use a placeholder name, and then try to change `column_ha` name with `my_var`, like this: col_list <- list(VAR = col_vector) names(col_list) <- my_var...meta_df <- data.frame(ID=paste0("id",rownames(iris_sub)), VAR=iris_sub[,ncol(iris_sub)]) names(meta_df)[2] <- my_var colnames(h…

ComplexHeatmap

updated 20 months ago • daniel.carbajo

div class="preformatted">Hi Alice, Please check the expression level of these negative control probes. They must be very low. If all the negative control probes are high, you might get a hybridizatin...alice.johnstone@esr.cri.nz> Subject: [BioC] What should happen to control probe information in bead level Illumina analyses? To: "bioconductor" <bioconductor at="" stat.math.ethz.ch="">…

probe probe

updated 17.7 years ago • Simon Lin

gt;= 7 table(isexpr) y0 <- y[y$genes$ControlType==0 & isexpr,] group <- SDRF[,"Dog"] levels <- c("1","2","3","4","5","6","7") group <- factor(group, levels = levels) type <- SDRF[,"Type"] levels <- c("P","M") type <- factor(type, levels = levels) design...lt;- lmFit(y0, design)</pre> It shows that <pre> Error in arra…

limma agilent microarrays lmfit

updated 9.4 years ago • Jesse L.

In trying to create a contrast matrix of interest, I thought it would be easier to assign one-word names to the different disease states. I seem to have gotten it to work for the GDS3715 data set that happens to be a 3x2 factorial...1] diabetes diabetes diabetes diabetes diabetes control control control [9] control control Levels: control diabetes > groups[groups=="control"]="Control" …

ASSIGN ASSIGN

updated 14.1 years ago • Voke AO

Sheet1", phenoDataDccColName = "ROI_ID", protocolDataColNames = c("Segment Tag", "Scan Name")) ``` Output: Error: `path` must be a string # please also include the results of running the following in an R session sessionInfo

HELP path

updated 16 months ago • cpierce2

Is range validity checked for when performing range operations on `GenomicRanges::GRanges

GenomicRanges

updated 6.3 years ago • Aditya

SYMBOL", multiVals = "list") # Filter genes that do not have valid or non-empty GO terms. empty_or_na_go_terms <- go_terms[sapply(go_terms, is_empty_or_na)] # Function to check if a vector...of GO terms is valid (not empty, non-null, and non-NA). has_valid_go_terms <- function(go_terms_vector) { !is.null(go_terms_vector) &am…

GO clusterProfiler enr

updated 14 months ago • Fatima

Hello, In a function for [plotting pairwise genome alignments](https://oist.github.io/GenomicBreaks/reference/makeOxfordPlots.html), I am concatenating all sequence levels of some GRanges objects. This can create seqlengths that are longer than what R's `integer` format can support. Unfortunately, my attempts to use the `numeric` format instead did not work as `seqlengths()` coerces its input …

GenomeInfoDb

updated 4.0 years ago • Charles Plessy

gene of interest This will be represented as a GRangesList, where each element in the list is a) named by the geneID b) contains a GRanges of the coordinates, name and id of each associated transcript All of this information...for one or more geneIDs, you want to ignore (for now) that gene information, and just extract the names of all of the transcripts. To do this extraction, you must flat…

updated 12.4 years ago • Paul Shannon

I have expression data with Affymetrix hg u133 plus 2 probeset IDs & gene set data with gene names. So both gene set and expression data are not using the same gene ID system which is a requirement to run the GAGE analysis...So the problem is that if i convert the Probeset IDs to gene name, i get a single gene name for multiple probes. So the expression data will now have multiple rows wi…

convert gage convert gage

updated 13.8 years ago • Javerjung Sandhu

analysis. Can anybody help me on this? Below is my sample dataset which has been taken from TCGA level 3 gene expression dataset of GBM (Cancer). Rownames are the genes names (ID).  <img alt="" src="https://dl.dropboxusercontent.com

limma microarray tcga

updated 10.6 years ago • hudacdif

is, is the LRT test calculating changes over time for every single organ given the the results name output below. I have re-leveled for time point to be the first time point, but haven't re-leveled for a specific organ as I am...Time_point + Organ ) dds <- DESeq(dds, reduced = ~Organ, test = "LRT")</pre> The results name is as follows: <pre> [1] "Intercept" …

DESeq2 LRT multiple time points

updated 7.7 years ago • A

deleted ] Patrick, I had a similar problem, and after some debugging I discovered that you must enter a valid groupName when calling BPMAPCelParser. You can get a list of the group names in the bpmap file by just looking

rMAT rMAT

updated 15.5 years ago • Larry Singh

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...y0 <- y[y$genes$ControlType==0 & isexpr,] Treatment <- SDRF[,"Characteristics[treatment]"] levels <- c("10 ml/kg saline",…

limma r

updated 9.4 years ago • Agaz Hussain Wani

summary stats, such as the percent positive events, to be drawn onto the xyplot in place of the gate name. I can get this to work fine with the following code for a single file, but I am having trouble getting the results for the...gt; subset = Filename == 327, scales=list(tick.number=10), outline=TRUE, -> names = format(summary(wf[["anothergate"]])$percent …

updated 16.7 years ago • Aric Gregson

Hi, An error occurred when I used the prePdata function: all (unlist (md_cols)% in% names (md)) is not TRUE: > sce <- prepData(samp, Panel, Sample_sheet, features = Panel$fcs_colname) Error in prepData(samp, Panel, Sample_sheet...Hi, An error occurred when I used the prePdata function: all (unlist (md_cols)% in% names (md)) is not TRUE: > sce <- pr…

cytofWorkflow

updated 2.8 years ago • shuangshuang

1.4.1 using command is for diff analysis without trans. discovery 'repA2.bam doesn't appear to be a valid BAM file' cuffdiff genes.gtf rep1.bam,rep2.bam \ repA2.bam,repA2.bam thanks in advance :) -- output of sessionInfo(): x -- Sent

updated 13.1 years ago • Guest User

I have expression data with Affymetrix hg u133 plus 2 probeset IDs & gene set data with gene names. So both gene set and expression data are not using the same gene ID system. Both gene set and expression data should use...is a requirement of the GAGE analysis. So the problem is that if i convert the Probeset IDs to gene name, i get a single gene name for multiple probes. So the expressio…

convert gage convert gage

updated 13.8 years ago • Javerjung Sandhu

Hello, At first, I must mention that I am a beginner in bioinformatics. I am really sorry since my questions may seem really basic. I am trying...Hello, At first, I must mention that I am a beginner in bioinformatics. I am really sorry since my questions may seem really basic. I am trying to...from my RNAseq data? I have read your article "Differential expression of RNA-Seq data at the gene l…

deseq2 differential gene expression bioconductor

updated 7.9 years ago • islamshaikhul2014

estimates and svalues for the same contrast dramatically change depending on the reference level. Here is a hopefully reproducible chunk of code based on [this txi object][1]: library(DESeq2) library(dplyr) #/ Load that txi...dds <- DESeq2::DESeq(dds, parallel = TRUE) #/ Version 1 with STHSC as reference level: dds$group <- relevel(dds$group…

DESeq2 apeglm

updated 4.8 years ago • ATpoint