How to annotate GPL for GEO data byhand?

Question

[MatthewP]

Hello, getGEO() function always fail to AnnoGPL for GSE69644. Error because

1: In download.file(myurl, destfile, mode = mode, quiet = TRUE, method = 
getOption("download.file.method.GEOquery")) :
  cannot open URL 'https://ftp.ncbi.nlm.nih.gov/geo/platforms/GPL13nnn/GPL13667/annot/GPL13667.annot.gz': 
HTTP status was '404 Not Found'

I want to know how can I annotate GPL information byhand? My expression matrix don't have probes ID because no GPL annotation.

> head(expr)
     GSM1705240 GSM1705241 GSM1705242 GSM1705243 GSM1705244 GSM1705245
NA      3.38697    3.30664    3.64258    3.67439    4.41090    4.34853
NA.1    4.79596    4.59640    4.92544    4.97072    5.39706    5.69815
NA.2    3.43121    3.39005    3.66856    3.61255    4.40618    4.39931
NA.3    4.28888    4.21054    3.33061    3.37118    3.62805    3.84138
NA.4    3.83599    3.50718    3.92205    3.49615    3.92734    3.56939
NA.5    3.09593    2.89687    2.91419    2.96769    3.15094    3.21477

Thanks

Answer 1

[Kevin Blighe]

I can easily download it here, using this code:

library(Biobase)
library(GEOquery)
gset <- getGEO("GSE69644", GSEMatrix =TRUE, getGPL=FALSE)
if (length(gset) > 1) idx <- grep("GPL13667", attr(gset, "names")) else idx <- 1
gset <- gset[[idx]]

head(exprs(gset))
              GSM1705240 GSM1705241 GSM1705242 GSM1705243 GSM1705244 GSM1705245
11715100_at      3.38697    3.30664    3.64258    3.67439    4.41090    4.34853
11715101_s_at    4.79596    4.59640    4.92544    4.97072    5.39706    5.69815
11715102_x_at    3.43121    3.39005    3.66856    3.61255    4.40618    4.39931
11715103_x_at    4.28888    4.21054    3.33061    3.37118    3.62805    3.84138
11715104_s_at    3.83599    3.50718    3.92205    3.49615    3.92734    3.56939
11715105_at      3.09593    2.89687    2.91419    2.96769    3.15094    3.21477

This array (Affy U219), however, does not appear to be in biomaRt, so, you could simply download the annotation table from HERE and use that to annotate it manually.

Kevin

[MatthewP]

Thanks a lot Kevin! This seems GSEMatrix(expression set) has probes id, why getGEO(filename="downloaded matrix txt") don't have probes id unless I use AnnotGPL=TRUE? This array information is on bioconduct hgu219.db which will helps me annotate gene names. Thank you again!

[tlaguna]

In my case, I needed all 3 options: getGPL=T + GSEMatrix=TRUE + AnnotGPL=T to retrieve the complete annotation for all the array probes.