I have RNA-seq from two sequencing batches; Lab technician says that he has run the RNA expression quantification two times in bathes 1 and 2 for example tumor 1 in batch 1 and tumor 1 in batch 2 , normal 2 in batch1 and normal 2 in batch 2
. This is my design for DESeq2
> head(mycols)
condition batch
N_1_305 N 1
N_1_310 N 1
N_1_337 N 1
N_1_353 N 1
T_1_305 T 1
T_1_310 T 1
> tail(mycols)
condition batch
T_2_337 T 2
T_2_338 T 2
T_2_344 T 2
T_2_346 T 2
T_2_349 T 2
T_2_353 T 2
>
I got this PCA plot
In PCA plot I am seeing for instance
, T_1_337 (batch1) has been placed too close to T_2_337 (batch2)
Then I used svd for detecting hidden batch
But from all these I did not understand too much
Does this mean that there is no big batch effect between experimental runs and I can concatenate the fastqs from both batches for each sample (technical replication) or collapse technical replicates afterwards?
Please help me to interpret these