Hello,

Thank you for the reply.

The spreadsheet 'Whole-genome DNA methylation profiling Annotations' has columns:
barcodes RID Phase Edate DateDrawn PlateNumber Array Slide

And, the methods PDF mentions:
"Normalized beta and M-value matrices TBD (pending availability)"

Reading one of the idat file:
List of 12
$ fileSize : num 13686999
$ versionNumber: int 3
$ nFields : int 19
$ fields : num [1:19, 1:3] 1000 102 103 104 107 200 300 400 401 402 ...
..- attr(*, "dimnames")=List of 2
.. ..$ : chr [1:19] "nSNPsRead" "IlluminaID" "SD" "Mean" ...
.. ..$ : chr [1:3] "fieldCode" "byteOffset" "Bytes"
$ nSNPsRead : int 1052641
$ Quants : int [1:1052641, 1:3] 18063 8350 5373 6961 950 10802 15204 12290 1913 2981 ...
..- attr(*, "dimnames")=List of 2
.. ..$ : chr [1:1052641] "1600101" "1600111" "1600115" "1600123" ...
.. ..$ : chr [1:3] "Mean" "SD" "NBeads"
$ MidBlock : int [1:1052641] 1600101 1600111 1600115 1600123 1600131 1600135 1600137 1600141 1600147 1600157 ...
$ RedGreen : int 0
$ Barcode : chr "200223270003"
$ ChipType : chr "BeadChip 8x5"
$ RunInfo : chr [1:20, 1:5] "10/20/2015 7:11:00 AM" "9/13/2016 11:47:50 AM" "9/13/2016 11:47:50 AM" "9/13/2016 11:47:50 AM" ...
..- attr(*, "dimnames")=List of 2
.. ..$ : NULL
.. ..$ : chr [1:5] "RunTime" "BlockType" "BlockPars" "BlockCode" ...
$ Unknowns :List of 7
..$ MostlyNull: chr ""
..$ MostlyA : chr "R07C01"
..$ Unknown.1 : chr ""
..$ Unknown.2 : chr ""
..$ Unknown.3 : chr ""
..$ Unknown.4 : chr ""
..$ Unknown.5 : chr ""

It's not clear to me where the timepoint information is.

Appreciate all the help.

Thanks

DateDrawn is the timepoint information.

Hello,

Thank you for the reply.

The spreadsheet 'Whole-genome DNA methylation profiling Annotations' has columns:
barcodes RID Phase Edate DateDrawn PlateNumber Array Slide

And, the methods PDF mentions:
"Normalized beta and M-value matrices TBD (pending availability)"

Reading one of the idat file:
List of 12
$ fileSize : num 13686999
$ versionNumber: int 3
$ nFields : int 19
$ fields : num [1:19, 1:3] 1000 102 103 104 107 200 300 400 401 402 ...
..- attr(*, "dimnames")=List of 2
.. ..$ : chr [1:19] "nSNPsRead" "IlluminaID" "SD" "Mean" ...
.. ..$ : chr [1:3] "fieldCode" "byteOffset" "Bytes"
$ nSNPsRead : int 1052641
$ Quants : int [1:1052641, 1:3] 18063 8350 5373 6961 950 10802 15204 12290 1913 2981 ...
..- attr(*, "dimnames")=List of 2
.. ..$ : chr [1:1052641] "1600101" "1600111" "1600115" "1600123" ...
.. ..$ : chr [1:3] "Mean" "SD" "NBeads"
$ MidBlock : int [1:1052641] 1600101 1600111 1600115 1600123 1600131 1600135 1600137 1600141 1600147 1600157 ...
$ RedGreen : int 0
$ Barcode : chr "200223270003"
$ ChipType : chr "BeadChip 8x5"
$ RunInfo : chr [1:20, 1:5] "10/20/2015 7:11:00 AM" "9/13/2016 11:47:50 AM" "9/13/2016 11:47:50 AM" "9/13/2016 11:47:50 AM" ...
..- attr(*, "dimnames")=List of 2
.. ..$ : NULL
.. ..$ : chr [1:5] "RunTime" "BlockType" "BlockPars" "BlockCode" ...
$ Unknowns :List of 7
..$ MostlyNull: chr ""
..$ MostlyA : chr "R07C01"
..$ Unknown.1 : chr ""
..$ Unknown.2 : chr ""
..$ Unknown.3 : chr ""
..$ Unknown.4 : chr ""
..$ Unknown.5 : chr ""

It's not clear to me where the timepoint information is.

Appreciate all the help.

Thanks