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wenbostar / metaX

metaX: a flexible and comprehensive software for processing omics data.
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questions about QC-based batch correction implemented in metaX package #4

Closed FSYtiredtodeath closed 6 years ago

FSYtiredtodeath commented 6 years ago

After reading metaX article, metaX manual and R documentation for this package, I have two major questions on methods for QC-based batch correction implemented in metaX R package.

  1. In this package, i guess there are two functions to do QC-based batch correction in metaX, namely 'doQCRLSC()' and the 'qcsc' argument in 'metaXpipe()' . As described in metaX_manual, the function 'doQCRLSC()' is used for QC-RSC normalization; and the argument 'qcsc' contains values including 'none', 'QC-RLSC' and 'SVR'. As QC-RSC(Quality Control-Robust Spline Correction) is a variation of QC-RLSC(Quality Control-Robust Loess Signal Correction) and they are obviously different methods, I wonder if doQCRLSC() and 'QC-RLSC' in 'qcsc' argument mean the same or different methods for batch correction ?
  2. If doQCRLSC() and 'QC-RLSC' in 'qcsc' argument mean the same method, then which method of QC-RLSC and QC-RSC is used in this package? Thanks a lot!
wenbostar commented 6 years ago

Hi @FSYtiredtodeath , the method implemented in doQCRLSC function is QC-RSC not QC-RLSC. I will update the description in the next version.

FSYtiredtodeath commented 6 years ago

Thanks a lot for your reply! @wenbostar

wenbostar commented 6 years ago

@FSYtiredtodeath , you're welcome. Please feel free to ask me if you have any questions about using metaX.

renzhezhu677 commented 6 years ago

Hi @wenbostar , I have a questions on reference for pqn implemented in metaX R package.What is the reference used in pqn? QC samples or Samples？

wenbostar commented 6 years ago

Could you please open an new issue for this question?