Two data set: Control sample is one data set and Case is another data with Time-series

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yuvayuvi369 • 0

@yuvayuvi369-23785

Last seen 3.8 years ago

I have two datasets

Dataset 1: Control Samples Dataset 2: Case Samples (time-series data - week 1, week 3 and week 8 treatment) Control and Case individuals are totally different

I would like to analyze these two data within groups (data) and between groups (data)

Comparison between Control vs week 1 Comparison between Control vs week 3 Comparison between Control vs week 8

Comparison between week 1 vs week 3 Comparison between week 1 vs week 8 Comparison between week 3 vs week 8

How to make comparisons (makeContrasts) in LIMMA? Do I need to consider it as paired or unpaired in LIMMA?

Do I need to use "duplicateCorrelation" function to treat control and case samples as a random effect?

Any help would be great!

Thank you in advance, Yuvaraj

LIMMA • 409 views

ADD COMMENT • link 3.8 years ago yuvayuvi369 • 0

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Please tell me that the RNA extractions and Illumina library preps for data set 1 and data set 2 happened at the same time...

ADD REPLY • link 3.8 years ago swbarnes2 ★ 1.3k

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This is a peptide array. All the experiments happened at the same time and batch.

ADD REPLY • link 3.8 years ago yuvayuvi369 • 0

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