Question: Can I colapsing raw read counts?
gravatar for jivarajivaraj
5 weeks ago by
jivarajivaraj10 wrote:

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

sva deseq2 R batch • 110 views
ADD COMMENTlink modified 4 weeks ago by Michael Love25k • written 5 weeks ago by jivarajivaraj10
Answer: Can I colapsing raw read counts?
gravatar for Michael Love
4 weeks ago by
Michael Love25k
United States
Michael Love25k wrote:

The two batches look very similar in the PCA plot above. If these are additional sequencing runs of the same sample, I would recommend to combine them. We have a function collapseReplicates in DESeq2 to perform the combination of technical replicates. Check out:

ADD COMMENTlink written 4 weeks ago by Michael Love25k
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