Dear all,
if I may ask for your opinions, and to double-check please : shall we have 2 RNA-seq samples
(sample1, sample2), and :
-- the same/ or distinct time points of COLLECTING the CELLS (of sample1, sample2), or
-- the same/ or distinct time points of SEQUENCING (of sample1, sample2),
in all these situations below, we shall correct for the BATCH EFFECTS, correct ? thank you !
SITUATION1 :
-- sample1: collection time A1, sequencing time B
-- sample2: collection time A2, sequencing time B
SITUATION2 :
-- sample1: collection time A, sequencing time B1
-- sample2: collection time A, sequencing time B2
SITUATION3 :
-- sample1: collection time A1, sequencing time B1
-- sample2: collection time A2, sequencing time B2
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Did you first check if there are any batch effects in the 3 situations?
hi Ashish.
On the actual data that we have, we do see big differences between the replicates on the PCA plot.
my question was a bit more general, in order to develop a better approach.
At this moment, 'm setting up a matrix, where we do have : SAMPLE; COLLECTION_TIME; SEQUENCING_TIME, planning to use the linear models in LIMMA.