Hi all,

I'm trying to analyse some methylation data that was taken from Illumina methylation EPIC microarray using lumi and I get the following error when I try to import my data. What could I be doing wrong? Any help is highly appreciated..

> library("lumi", lib.loc="C:/R-3.3.0beta/library")

> sampleInfo=read.csv("E:/A/200357150012/SAM18211 mthylation EPIC.txt",sep="\t", header=T, stringsAsFactors=F)

> sampleInfo
           Header.                       
1  Investigator Name                               
2       Project Name                               
3    Experiment Name                               
4               Date                      8/26/2012
5        [Manifests]                               
6                  A MethylationEPIC_15073387_v-1-0
7             [Data]                               
8        Sample_Name                   Sample_Group
9         75-1482LAD                              A
10       75-1606LAC1                              B
11       75-1607LAC2                              C
12       121-1484LAD                              A
13      121-1608LAC1                              B
14      121-1610LAC2                              C
15        139-1485AD                              A
16       139-1611AC1                              B
           
8  Sample_Plate  Project Pool_ID Sample_Well  SENTRIX_ID
9            73 SAM18211       0         A10 2.00357E+11
10           74 SAM18211       0         B10 2.00357E+11
11           75 SAM18211       0         C10 2.00357E+11
12           76 SAM18211       0         D10 2.00357E+11
13           77 SAM18211       0         E10 2.00357E+11
14           78 SAM18211       0         F10 2.00357E+11
15           79 SAM18211       0         G10 2.00357E+11
16           80 SAM18211       0         H10 2.00357E+11
        
8  SENTRIX_POSITION
9            R01C01
10           R02C01
11           R03C01
12           R04C01
13           R05C01
14           R06C01
15           R07C01
16           R08C01
> data=importMethyIDAT(sampleInfo, dataPath = getwd(), lib = NULL, bigMatrix=FALSE, dir.bigMatrix='.')
Error in importMethyIDAT(sampleInfo, dataPath = getwd(), lib = NULL, bigMatrix = FALSE,  : 

  'SENTRIX_POSITION' and 'SENTRIX_BARCODE' or 'SENTRIX_ID' and are required in 'sampleInfo'!

Thanks,

Rasi

That's sort of weird. This is what is supposed to happen:

 if (any(colnames(sampleInfo) == "SENTRIX_ID") && !("SENTRIX_BARCODE" %in%
            colnames(sampleInfo))) {
            colnames(sampleInfo)[colnames(sampleInfo) == "SENTRIX_ID"] <- "SENTRIX_BARCODE"
        }

So the column labeled 'SENTRIX_ID' is supposed to be renamed 'SENTRIX_BARCODE', and things are supposed to proceed from there. But the very next code block is this:

if (!all(c("SENTRIX_BARCODE", "SENTRIX_POSITION") %in%
            colnames(sampleInfo))) {
            stop("'SENTRIX_POSITION' and 'SENTRIX_BARCODE' or 'SENTRIX_ID' and are required in 'sampleInfo'!")
        }

Which is basically indicating that the first code block isn't correctly renaming the column. But whatever. You should just be able to rename by hand and have it work.