Getting information about samples(.CEL files) from GEO using R

Question

[osiemen]

Hello all,

Using the GEOquery library in R I have managed to download 850 samples I am interested in. I used the following code for this:

x <- as.list(scan("fileWithGEOsampleAccesionCodes.txt", what ="" , sep = "" ))

data= lapply(x,getGEOSuppFiles)

I have read the CEL files into an affyBatch using - > r <- ReadAffy(celfile.path = pathToFiles,compress = TRUE)

I want to look which micro-array platform is being for each sample. With micro-array platform I mean --> AffyA , AffyPlus2 , also know as hgu133a ,hgu133plus2 .

How can I do this using the data I already have or using the accessioncodes? Basically I want to know the annotation for each sample (.CEL file) .

Thank you in advance!

Answer 1

[Kevin Blighe]

If you just have a list of the CEL files, then you should be able to get this via the CDF entry in the CEL header with:

CELFiles
 [1] "SampleFiles//AC31_(BovGene-1_0-st).CEL"          
 [2] "SampleFiles//AC32+AC33_(BovGene-1_0-st).CEL"     
 [3] "SampleFiles//AC33+AC32_(BovGene-1_0-st).CEL"     
 [4] "SampleFiles//AC33+OA23_(BovGene-1_0-st).CEL"     
 [5] "SampleFiles//AC34_(BovGene-1_0-st).CEL"          
 [6] "SampleFiles//NL13_(BovGene-1_0-st).CEL"          
 [7] "SampleFiles//NL14_(BovGene-1_0-st).CEL"          
 [8] "SampleFiles//NL16_(BovGene-1_0-st).CEL"          
 [9] "SampleFiles//NL17_(BovGene-1_0-st).CEL"          
[10] "SampleFiles//NM1_(BovGene-1_0-st).CEL"           
[11] "SampleFiles//NM2_(BovGene-1_0-st).CEL"           
[12] "SampleFiles//NM3_(BovGene-1_0-st).CEL"           
[13] "SampleFiles//NM41_(BovGene-1_0-st).CEL"          
[14] "SampleFiles//NM42_(BovGene-1_0-st).CEL"          
[15] "SampleFiles//NM43_(BovGene-1_0-st).CEL"          
[16] "SampleFiles//NM44_(BovGene-1_0-st).CEL"          
[17] "SampleFiles//NM4_(BovGene-1_0-st).CEL"           
[18] "SampleFiles//OA21_(BovGene-1_0-st).CEL"          
[19] "SampleFiles//OA22+OA23+OA24_(BovGene-1_0-st).CEL"
[20] "SampleFiles//OA22+OA24_(BovGene-1_0-st-v1).CEL"  
[21] "SampleFiles//OA23+AC32_(BovGene-1_0-st-v1).CEL"  
[22] "SampleFiles//OA24+OA22_(BovGene-1_0-st-v1).CEL"  


require(affy)
data.frame(CELFiles, unlist(lapply(CELFiles, function(x) affyio::read.celfile.header(x)[["cdfName"]])))
                                           CELFiles  Type
1            SampleFiles//AC31_(BovGene-1_0-st).CEL  BovGene-1_0-st
2       SampleFiles//AC32+AC33_(BovGene-1_0-st).CEL  BovGene-1_0-st
3       SampleFiles//AC33+AC32_(BovGene-1_0-st).CEL  BovGene-1_0-st
4       SampleFiles//AC33+OA23_(BovGene-1_0-st).CEL  BovGene-1_0-st
5            SampleFiles//AC34_(BovGene-1_0-st).CEL  BovGene-1_0-st
6            SampleFiles//NL13_(BovGene-1_0-st).CEL  BovGene-1_0-st
7            SampleFiles//NL14_(BovGene-1_0-st).CEL  BovGene-1_0-st
8            SampleFiles//NL16_(BovGene-1_0-st).CEL  BovGene-1_0-st
9            SampleFiles//NL17_(BovGene-1_0-st).CEL  BovGene-1_0-st
10            SampleFiles//NM1_(BovGene-1_0-st).CEL  BovGene-1_0-st
11            SampleFiles//NM2_(BovGene-1_0-st).CEL  BovGene-1_0-st
12            SampleFiles//NM3_(BovGene-1_0-st).CEL  BovGene-1_0-st
13           SampleFiles//NM41_(BovGene-1_0-st).CEL  BovGene-1_0-st
14           SampleFiles//NM42_(BovGene-1_0-st).CEL  BovGene-1_0-st
15           SampleFiles//NM43_(BovGene-1_0-st).CEL  BovGene-1_0-st
16           SampleFiles//NM44_(BovGene-1_0-st).CEL  BovGene-1_0-st
17            SampleFiles//NM4_(BovGene-1_0-st).CEL  BovGene-1_0-st
18           SampleFiles//OA21_(BovGene-1_0-st).CEL  BovGene-1_0-st
19 SampleFiles//OA22+OA23+OA24_(BovGene-1_0-st).CEL  BovGene-1_0-st
20   SampleFiles//OA22+OA24_(BovGene-1_0-st-v1).CEL  BovGene-1_0-st
21   SampleFiles//OA23+AC32_(BovGene-1_0-st-v1).CEL  BovGene-1_0-st
22   SampleFiles//OA24+OA22_(BovGene-1_0-st-v1).CEL  BovGene-1_0-st