Question: Illumina 450K quality controls with meffil
0
gravatar for uxue33
11 days ago by
uxue330
uxue330 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

methylation ewas meffil • 34 views
ADD COMMENTlink modified 11 days ago by James W. MacDonald51k • written 11 days ago by uxue330

Cross-posted: https://www.biostars.org/p/402202/

ADD REPLYlink written 11 days ago by Kevin Blighe200
Answer: Illumina 450K quality controls with meffil
0
gravatar for James W. MacDonald
11 days ago by
United States
James W. MacDonald51k wrote:

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.

ADD COMMENTlink written 11 days ago by James W. MacDonald51k
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