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Vitalina Komashko (Unlicensed)

Vitalina Komashko (Unlicensed)

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        Here are a few lines from the final targets file. The only important column is Basename that indicates where the files are for every patients if _Grn.idat or _Red.idat can be attached. I have other information because it is convenient to have it later for data normalization.

Code Block
collapsetrue
Sample_Name = patient barcode
Sample_Well = center (2nd field in the barcode)
Sample_Plate = BCR barcode (6th field in the barcode)
Sample_Group = sample type (normal/tumor)
Pool_ID = processing batch (TCGA archive name)
Array = array on a slide
Slide = slide that contains 12 arrays
Basename = path to the directory with files
 
>head(targets)
Sample_Name Sample_Well Sample_Plate Sample_Group Pool_ID  Array      Slide
1 TCGA-A6-4107-01A-02D-1407-05          A6         1407        tumor   1.1.0 R01C01 5775041065
2 TCGA-AA-3510-01A-01D-1407-05          AA         1407        tumor   1.1.0 R02C01 5775041065
3 TCGA-AZ-4308-01A-01D-1407-05          AZ         1407        tumor   1.1.0 R03C01 5775041065
4 TCGA-A6-2679-01A-02D-1407-05          A6         1407        tumor   1.1.0 R04C01 5775041065
5 TCGA-AZ-4682-01B-01D-1407-05          AZ         1407        tumor   1.1.0 R05C01 5775041065
6 TCGA-AA-3492-01A-01D-1407-05          AA         1407        tumor   1.1.0 R06C01 5775041065
                                                                Basename
1 ./DNA_Methylation/JHU_USC__HumanMethylation450/Level_1/5775041065_R01C01
2 ./DNA_Methylation/JHU_USC__HumanMethylation450/Level_1/5775041065_R02C01
3 ./DNA_Methylation/JHU_USC__HumanMethylation450/Level_1/5775041065_R03C01
4 ./DNA_Methylation/JHU_USC__HumanMethylation450/Level_1/5775041065_R04C01
5 ./DNA_Methylation/JHU_USC__HumanMethylation450/Level_1/5775041065_R05C01
6 ./DNA_Methylation/JHU_USC__HumanMethylation450/Level_1/5775041065_R06C01
Colnames descriptions:

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Sample_Name = patient barcode
Sample_Well = center (2nd field in the barcode)
Sample_Plate = BCR barcode (6th field in the barcode)
Sample_Group = sample type (normal/tumor)
Pool_ID = processing batch (TCGA archive name)
Array = array on a slide
Slide = slide that contains 12 arrays
Basename = path to the directory with files

 

    3. Read the files

Code Block
collapsetrue
> library(minfi) 
> RGset<-read.450k.exp(targets=targets)

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