Question: Some terms in EPIC Methylation Analysis
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gravatar for yuabrahamliu
9 months ago by
yuabrahamliu0 wrote:

Hi there,

Maybe this is a silly question, but it really made me confused. When use ChAMP to analyze EPIC methylation data, the SVD step will display the significant components of variation in the result heatmap. The components always include Sample Plate, Array and Slide. However, I don't know exactly what is Sample Plate, what is Array and what is Slide. As far as I known, a Slide contains several Arrays on it and each Array corresponds to a sample. Is it right? But what is Sample Plate and what is the relationship between these components?

Thank you so much.

champ array svd slide sample plate • 210 views
ADD COMMENTlink modified 9 months ago by Yuan Tian110 • written 9 months ago by yuabrahamliu0
Answer: Some terms in EPIC Methylation Analysis
0
gravatar for Yuan Tian
9 months ago by
Yuan Tian110
University College London
Yuan Tian110 wrote:

Hello

"Array" and "Slides" are extracted from sample sheet information, with column names Sentrix_ID and Sentrix_Position, the names are get changed during loading. While sample_plate is one column in sample_sheet.

According to minfi's vignette:  "Physically, each sample is measured on a single “array”. There are 12 arrays on a single physical “slide” (organized in a 6 by 2 grid). Slides are organized into “plates” containing at most 8 slides (96 arrays)."

SVD check relationship between all factors and components, assuming that they all could be account for variance exist in data set.

Best

Yuan Tian

ADD COMMENTlink written 9 months ago by Yuan Tian110

Really helpful! Thank you so much!

ADD REPLYlink written 9 months ago by yuabrahamliu0
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