Issue loading target files

[VilainLab]

Hi,

I am having a strange issue. when using read.metharray.sheet function it dose not read the basename for multiple cells, but reads all the other cells correctly.

targets <- read.metharray.sheet(testDir, pattern=".csv$") [read.metharray.sheet] Found the following CSV files: [1] "X:/Suro/Methylation/Methylation_06232019/PLA_vs_CTL_P1.csv"

Just the basenames

targets$Basename[1:15] [1] "X:/Suro/Methylation/Methylation_06232019/idat/203286230205/203286230205_R07C01" [2] "X:/Suro/Methylation/Methylation_06232019/idat/203286230205/203286230205_R08C01" [3] "X:/Suro/Methylation/Methylation_06232019/idat/203271750128/203271750128_R04C01" [4] "X:/Suro/Methylation/Methylation_06232019/idat/203271750128/203271750128_R05C01" [5] "X:/Suro/Methylation/Methylation_06232019/idat/203271750128/203271750128_R06C01" [6] "X:/Suro/Methylation/Methylation_06232019/idat/203271750128/203271750128_R07C01" [7] "X:/Suro/Methylation/Methylation_06232019/idat/203271750128/203271750128_R08C01" [8] "character(0)"
[9] "character(0)"
[10] "character(0)"
[11] "character(0)"
[12] "character(0)"
[13] "X:/Suro/Methylation/Methylation_06232019/idat/203287590116/203287590116_R01C01" [14] "X:/Suro/Methylation/Methylation_06232019/idat/203287590117/203287590117_R01C01" [15] "X:/Suro/Methylation/Methylation_06232019/idat/203287590117/203287590117_R02C01"

All the columns for row 8 and row 9

targets[8:9,] Sample_Name Sample_Well Sample_Plate Sample_Group Pool_ID Project Array Slide Type Status Basename 8 PLA-P1-0013 B9 PLA LIMP_1 LIMP R02C01 203481950084 CHK P1 character(0) 9 PLA-P1-0018 C9 PLA LIMP_1 LIMP R03C01 203481950084 CHK P1 character(0)

when I just read its a csv I have values in place of the character(0).

r1 <- read.csv( "X:/Suro/Methylation/Methylation_06232019/PLA_vs_CTL_P1.csv") r1$Basename [1] X:/Suro/Methylation/Methylation_06232019/idat/203286230205/203286230205_R07C01 [2] X:/Suro/Methylation/Methylation_06232019/idat/203286230205/203286230205_R08C01 [3] X:/Suro/Methylation/Methylation_06232019/idat/203271750128/203271750128_R04C01 [4] X:/Suro/Methylation/Methylation_06232019/idat/203271750128/203271750128_R05C01 [5] X:/Suro/Methylation/Methylation_06232019/idat/203271750128/203271750128_R06C01 [6] X:/Suro/Methylation/Methylation_06232019/idat/203271750128/203271750128_R07C01 [7] X:/Suro/Methylation/Methylation_06232019/idat/203271750128/203271750128_R08C01 [8] X:/Suro/Methylation/Methylation_06232019/idat/203481950084/203481950084_R02C01 [9] X:/Suro/Methylation/Methylation_06232019/idat/203481950084/203481950084_R03C01 [10] X:/Suro/Methylation/Methylation_06232019/idat/203481950084/203481950084_R04C01 [11] X:/Suro/Methylation/Methylation_06232019/idat/203481950084/203481950084_R05C01 [12] X:/Suro/Methylation/Methylation_06232019/idat/203481950084/203481950084_R06C01 [13] X:/Suro/Methylation/Methylation_06232019/idat/203287590116/203287590116_R01C01 [14] X:/Suro/Methylation/Methylation_06232019/idat/203287590117/203287590117_R01C01 [15] X:/Suro/Methylation/Methylation_06232019/idat/203287590117/203287590117_R02C01 r1[8:9,] Sample_Name Sample_Well Sample_Plate Sample_Group Pool_ID Project Array Slide Type Status 8 PLA-P1-0013 B9 NA PLA LIMP_1 LIMP R02C01 2.03482e+11 CHK P1 9 PLA-P1-0018 C9 NA PLA LIMP_1 LIMP R03C01 2.03482e+11 CHK P1 Basename 8 X:/Suro/Methylation/Methylation_06232019/idat/203481950084/203481950084_R02C01 9 X:/Suro/Methylation/Methylation_06232019/idat/203481950084/203481950084_R03C01

I have already run a few samples earlier using the minfi, and never faced this issue before.

Please let me know, if you need any other informatiuon to debug this?

Thanks, Surajit PLA_vs_CTL_P1.txt

[wvictor14]

read.metharray.sheet will try to find associated idat files based on the Array and Slide columns and your supplied base directory (i.e. the string object testDir in your code),

The entries

character(0)

indicate there are no associated idats found @ the location X:/Suro/Methylation/Methylation_06232019/idat/. Can you manually navigate to those folders and check if idats for these samples are there?

[VilainLab]

Hello,

Thanks a lot. that solves the issue,

Surajit