What this error means?Error in getEAWP(object) : data object isn't of a recognized data class

Question

[Sib]

I am performing differential expression analysis by R. After constructing design when I entered

>  fit<- lmFit(gset,design)

I got the error "Error in getEAWP(object) : data object isn't of a recognized data class" here is my total sorce code:

    >  setwd("E:/microarray/")
    >  library(Biobase)
    >  library(GEOquery)
    >  library(ggplot2)
    >  library(pheatmap)
    >  gset<-getGEO("GSE116959",GSEMatrix = TRUE,AnnotGPL = TRUE,destdir ="data/")
    >  gset<-gset[[1]]
    >  gr<-c(rep("Tumor",3),("Normal"),rep("Tumor",7),("Normal"),rep("Tumor",21),rep("Normal",4)
          ,rep("Tumor",5),("Normal"),rep("Tumor",17),rep("Normal",2),("Tumor"),("Normal"),rep("Tumor",2), 
          ("Normal"),`("Tumor"))`
    >  gr<-factor(gr)
    >  gset$description<-gr
    >  design<-model.matrix(~description+0,gset)
    >  colnames(design)<-levels(gr)
    >  fit<-lmFit(gset,design)

[Jean-Karim Heriche]

From the lmFit doc:

Arguments
object: A matrix-like data object containing log-ratios or log-expression values for a series of arrays, with rows corresponding to genes and columns to samples. Any type of data object that can be processed by getEAWP is acceptable.

From the getEAWP doc:

getEAWP will return an error if object is a non-normalized data object such as RGList or EListRaw, because these do not contain log-expression values.

[Sib]

But my data was normalized at GEO.

[Jean-Karim Heriche]

Possibly but is it an object of a class accepted by limma? From the getGEO doc:

Value: An object of the appropriate class (GDS, GPL, GSM, or GSE) is returned...

Read the GEOquery vignette section on Converting to BioConductor ExpressionSets and limma MALists

Anyway, I would suggest starting from the raw values if possible.

[Sib]

I ran the commands from the over and my problem was fixed. I did not understand what happened exactly but I appreciate you for trying to help me.

[anasjamshed]

brother i want complete code for practice

Answer 1

[ATpoint]

The code runs without error on my machine (Mac OS) after removing these quotations outside of the last tumor when defining gr. Can you try on a Unix system?

[Sib]

You are right. I ran the commands from the over and my problem was fixed. I don't know the first time what was wrong.

[ATpoint]

Probably a variable in the environment with a wrong content. Happens to all of us :) Good to hear it works now.

[Gordon Smyth]

I suspect you missed out gset <- gset[[1]] the first time, meaning that gset would be a list rather than an ExpressionSet. That would produce the error message from limma.