Getting information about samples(.CEL files) from GEO using R
1
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!
micro-array
R
• 2.4k views
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
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