Follow-Up Question: How To Import Annotation File Into R?

Question

[jobinv]

As a follow-up question to Where to find annotation file for Agilent microarray? :

Does anyone have any tips as to how I can import this to R? The regular read.table command isn't working because not all features have entries in all fields, causing errors such as this one:

read.table("../../../del/014850_D_AA_20070207.txt",sep="\t")
Error in scan(file, what, nmax, sep, dec, quote, skip, nlines, na.strings,  : 
  line 155 did not have 14 elements

[Olivier]

My best guess is you probably have to clean it up (e.g. with awk or grep) or specify na.strings = "the char that is na" as argument in your read.table()?
Did you try AILUN as we did previously, to get annotations?

[jobinv]

No, didn't even think of AILUN actually, good point. Should see whether that can solve my issue.

Answer 1

[David Westergaard]

What not use the Bioconductor package instead?

If you insist on using read.table, try changing the comment parameter:

read.table("../../../del/014850_D_AA_20070207.txt",sep="\t",comment.char='')

[jobinv]

Wow, didn't realize there was one! Thanks!