Question: Lumi error in importMethylIDAT
0
gravatar for rasii
3.4 years ago by
rasii0
rasii0 wrote:

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

lumi illumina methylation • 546 views
ADD COMMENTlink modified 3.4 years ago by James W. MacDonald51k • written 3.4 years ago by rasii0
Answer: Lumi error in importMethylIDAT
0
gravatar for James W. MacDonald
3.4 years ago by
United States
James W. MacDonald51k wrote:

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.

ADD COMMENTlink written 3.4 years ago by James W. MacDonald51k
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 16.09
Traffic: 119 users visited in the last hour