Question

Question Posted 07/12/17:
Hello,

I was wondering when the Normalized beta and M-value matrices for DNA Methylation data be available?

And, is there timepoint information in the SampleAnnotation file?

Thanks
Response posted 07/13/17 by sharvari gujja:
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
Response posted 07/13/17 by Kwangsik Nho:
DateDrawn is the timepoint information.
Response posted 07/13/17 by sharvari gujja:
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