Home/ Questions/Q 8422865
In Process

The Archive Base Latest Questions

Editorial Team
  • 0
Asked: 2026-06-10T03:34:30+00:00

I am using a package from Biobase : arrayQualityMetrics for creating the plots for

  • 0

I am using a package from Biobase : arrayQualityMetrics for creating the plots for visualization of microarray data.

My data is stored in ExpressionSet.
one of the column names of the phenoData(ExpressionSet) has name “Tissue” but when i run the following command : 

arrayQualityMetrics(ExpressionSet,intgroup = "Tissue")

It gives me an error saying that : 

Error in prepdata(expressionset, intgroup = intgroup, do.logtransform = do.logtransform) : 
  all elements of 'intgroup' should match column names of 'pData(expressionset)'.

I dont understand why I ma getting this error although my ExpressionSet contains a column names “Tissue” in its phenoData.

Share

Leave an answer

You must login to add an answer.

Need An Account,

1 Answer

  1. Editorial Team

    It’s been awhile since you asked this question but this is likely due to arrayQualityMetrics() having to trim down the data frame in your pData() slot to a limited number of fields for display in the metadata table at the beginning of the report.

    Try something like:

    tmp <- pData(ExpressionSet)
pData(ExpressionSet) <- tmp[,c("Tissue", "SomeOtherInterestingField")] # swap out
arrayQualityMetrics(ExpressionSet,intgroup="Tissue")
pData(ExpressionSet) <- tmp # replace with your original full pData() data frame
    • 0