Question: about the batch effects
0
gravatar for Bogdan
10 months ago by
Bogdan1.0k
Palo Alto, CA, USA
Bogdan1.0k wrote:

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

rna-seq • 237 views
ADD COMMENTlink modified 8 months ago by swbarnes28.9k • written 10 months ago by Bogdan1.0k

Did you first check if there are any batch effects in the 3 situations?

ADD REPLYlink written 10 months ago by ashish540

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.

ADD REPLYlink written 10 months ago by Bogdan1.0k
0
gravatar for swbarnes2
8 months ago by
swbarnes28.9k
United States
swbarnes28.9k wrote:

In general, running the same library at different times is not going to cause a batch effect. So don't worry about when you sequence. Do collect all the RNA at around the same time, and do make all the library preps at the same time, as much as you are able.

ADD COMMENTlink written 8 months ago by swbarnes28.9k
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