Question: Illumina 450K quality controls with meffil
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gravatar for uxue33
12 days ago by
uxue3320
uxue3320 wrote:

I'm trying to run quality control on the Illumina 450K methylation chip data with the meffil package.

I create the Sample sheet using the following command:

samplesheet <- meffil.create.samplesheet("/path/to/idat/files/", recursive=TRUE)

I add sex and personal id columns and load again with this command:

  samplesheet <- meffil.read.samplesheet(base="/path/to/samplesheet/",pattern = "SampleSheet_450K.csv")

I get this error when running the code above:

[read.450k.sheet] Found the following CSV files:
[1] "/.../SampleSheet_450K.csv"
Warning message:
In FUN(X[[i]], ...) :
  Could not infer array name for file: /.../SampleSheet_450K.csv

Any advice or clue is more than welcome, is my first time doing this kind of analyses.

Thanks in advance for your help,

Uxue

meffil snp ewas • 72 views
ADD COMMENTlink written 12 days ago by uxue3320
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