This is a test version of Biostars. For the public version, visit https://www.biostars.org.
Error in validObject(.Object) : invalid class “ExpressionSet” object: sampleNames differ between assayData and phenoData

Hi Biostar,

I try to perform Differential expression at pathway level:

 disease_es <- gsva(disease_Par)

Error in validObject(.Object) : 
  invalid class “ExpressionSet” object: sampleNames differ between assayData and phenoData

https://bioconductor.org/packages/devel/bioc/vignettes/GSVA/inst/doc/GSVA.html
Seem the error is because the colnames(gene_expression) is not in the same or order of rownames(p_Data). I found an similar issue here: https://support.bioconductor.org/p/84162/
Would you please have a suggestion to fix this error? Thank you so much!

With some manipulate the name, I reordered it to match and no more error.

gsva
• 937 views • link
written by Chris • Chris

0 answers

No answers yet.

Log in to answer this question.

More posts like this
  • Differential expression at pathway level
    written by Chris • Chris
    Hi Biostar, I would like to do differential expression at pathway level by following this tutorial. I have microarray data. Would you please tell me …
  • Using GEOquery
    written by Aryan • Aryan
    Hello, I am trying to access data for all 404 samples in the GEO entry [GSE120742][1] using GEOquery on R. My steps are, ```r library(GEOquery) …
  • Cannot instantiate ExpressionSet
    written by hansrupp • hansrupp
    Hello, I am a beginner with bioinformatics.. I am trying to follow https://app.datacamp.com/learn/courses/differential-expression-analysis-with-limma-in-r library(tidyverse) rm(list=ls()) BiocManager::install("breastCancerVDX") #https://bioconductor.org/packages/release/data/experiment/html/breastCancerVDX.html library(breastCancerVDX) library(Biobase) # load the dataset data(vdx) eset …
  • Where to find annotation infos for my Expressionset?
    written by loicborcard01 • loicborcard01
    Hello, I am running gsva on an ExpressionSet and a Geneset.collection that I created myself. And I get the error message written in red down …
  • crlmm problem: NChannelSet error
    written by scott.hazelhurst • scott.hazelhurst
    I am trying to use crlmm to process some idat files. Using genotype.illumina I get the following error. Error in validObject(.Object) : invalid class “NChannelSet” …
  • eqtl using ggtools
    written by Omics data mining Omics data mining
    Hi everyone I am trying to run GGtools for prediction of eqtl based on the genotypes and expression information. https://bioconductor.org/packages/release/bioc/vignettes/GGtools/inst/doc/GGtools.pdf I am trying to run …
  • Creation of cellDataSet in Monocle 2 wants undocumented AnnotatedDataFrame: assayData
    written by mk mk
    As directed in the [Monocle 2 Documentation][1], the cellDataSet constructor is called on a sparse matrix and two AnnotatedDataFrames. Here is the suggested usage: pd …
  • Analyse of HGU133 set microarrays / Merge ExpressionSets
    written by giroudpaul giroudpaul
    Hello, I am currently trying to extract data from a GEO dataset which has been done on the Affymetrix HGU133 plateforme, meaning that all samples …
  • blood deconvolution - cellmix
    written by kuragari.ch • kuragari.ch
    Dear all, I want to perform the deconvolution of a set of blood samples (microarray). Hence I tried to use `CellMix`. Beeing `tapas2` my data-set: …
  • Geoquery And Gse Error
    written by Avoks • Avoks
    <p>Hi all,</p> <p>I am unable to access a series file even though I get a message that it saved to a local directory, albeit with …