Illumina 450K quality controls with meffil
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uxue33 • 0
@uxue33-22098
Last seen 20 months ago

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 EWAS methylation • 212 views
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@james-w-macdonald-5106
Last seen 16 minutes ago
United States

While Meffil uses some Bioconductor packages, it is not a Bioconductor package. This support site is intended for Bioc packages, not general questions. Plus as Kevin Blighe noted, cross-posting is considered bad form. For a GitHub package you should probably contact the maintainer directly rather than using various support sites, because the maintainer is best suited to actually provide help.

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