Microarray Error
1
0
Entering edit mode
7 days ago
rpazo001 ▴ 20

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.

R Microarray • 136 views
ADD COMMENT
0
Entering edit mode

Solved issue . Thank you.

ADD REPLY
0
Entering edit mode

Please edit the post above and include the solution you found. Without the solution this thread remains incomplete and will not be useful to a future visitor who finds this by a search.

ADD REPLY
2
Entering edit mode
6 days ago
rpazo001 ▴ 20

Solution:

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

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

Login before adding your answer.

Traffic: 2445 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6