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.

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