Microarray Error

Question

[rpazo001]

Hi everyone,

I am a student learning how to do microarray analysis and R. I am trying to process CEL files with "affy" so the program directory knows how it can find the CEL files and the corresponding file with phenoData. The first part of the code works find ( creating the dataframe for my.pdata), but when I keep going to finish the processing I get the following errors:

 #### Head ERROR####
> head(my.pdata[, c("title", "geo_accession", "description")], 10)
Error in h(simpleError(msg, call)) : 
  error in evaluating the argument 'x' in selecting a method for function 'head': undefined columns selected
> 
> my.pdata <- my.pdata[, c("title", "geo_accession", "description")]
Error in `[.data.frame`(my.pdata, , c("title", "geo_accession", "description")) : 
  undefined columns selected

I was wondering if anyone can tell me what I am doing wrong. I was following the script listed in https://www.stat.purdue.edu/bigtap/online/docs/Introduction_to_Microarray_Analysis_GSE15947.html (section part 4), but I am using a different dataset. Thank you for your time.

[rpazo001]

Solved issue . Thank you.

[GenoMax]

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Answer 1

[rpazo001]

Solution:

> head(my.pdata[, c("title", "geo_accession", "status")], 10)

> my.pdata <- my.pdata[, c("title", "geo_accession", "status")]