Batch effect correction of RNA-Seq data

0

Hi all,

I want to integrate RNA-seq data from 2 studies. My plan is to merge the count matrices and then perform batch effect correction using Combat-seq. However, while study A has samples at different ages and sex, the age and sex of the samples in study B is unknown. Also, study A has samples from 2 tissues but study B only from 1. Do you have any advice on how should I proceed? I have two options in mind.

  1. Consider each sub-dataset (samples grouped by batch, sex, age and tissue) as a different batch. Study B is the same batch.
  2. Forget about age and sex and only group by batch and tissue, so there are 4 batches for study A and 1 for study B

Toy example (I have more samples from each case):

study batch group   age sex  tissue
  A     1   control 10   M   cortex  
  A     2   control 10   F   cortex
  A     1   control 20   M   cortex
  A     2   control 20   F   cortex
  A     1   cases   10   M   cortex  
  A     2   cases   10   F   cortex
  A     1   cases   20   M   cortex
  A     2   cases   20   F   cortex
  A     1   control 10   M   cerebellum  
  A     2   control 10   F   cerebellum
  A     1   control 20   M   cerebellum
  A     2   control 20   F   cerebellum
  A     1   cases   10   M   cerebellum  
  A     2   cases   10   F   cerebellum
  A     1   cases   20   M   cerebellum
  A     2   cases   20   F   cerebellum
  B     3   control -    -   cortex  
  B     3   control -    -   cortex
  B     3   control -    -   cortex
  B     3   control -    -   cortex
  B     3   cases   -    -   cortex  
  B     3   cases   -    -   cortex
  B     3   cases   -    -   cortex
  B     3   cases   -    -   cortex

Thanks a lot


batch-effect


R


RNA-seq

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4 hours ago by


Geo

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