Closed:Can I colapsing raw read counts?
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@fereshteh-15803
Last seen 11 months ago
United Kingdom

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

enter image description here

And this is biplot of samples enter image description here

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

enter image description here

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

deseq2 r batch sva • 216 views
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