Greeting Members
I have an experiment with 4 time points and 5 biological replicates and each biological replicate has 5 technical replicates (100 samples thus)
The first two time points are really early is the organism's life cycle and hence we often expect less reads for some genes:
After summing the reads from the technical replicates, I get this profile (OBVIOUSLY AN ARTEFACT)
0h GeneA 3 reads
0h GeneA 2 reads
0h GeneA 0 reads
0h GeneA 1 reads
0h GeneA 3 reads
24h GeneA 0 reads
24h GeneA 1 reads
24h GeneA 2 reads
24h GeneA 0 reads
24h GeneA 1 reads
But DeSeq2 analysis of DE of these genes gives me a profile like this:
baseMean log2FoldChange lfcSE stat pvalue padj
31.88739159 -4.026822896 0.943450084 -4.268188603 1.97E-05 0.007173227
How do I filter for such artefacts ? Though I give an example here, my results are severely afflicted with these kind of low read count but highly significant statistics.
Any suggestion is highly appreciated...
I cannot set a minreadcount filter as these genes will have higher read count as the time line progresses (and will also skew the stats if I only remove it for one time point)
I have an experiment with 4 time points and 5 biological replicates and each biological replicate has 5 technical replicates (100 samples thus)
The first two time points are really early is the organism's life cycle and hence we often expect less reads for some genes:
After summing the reads from the technical replicates, I get this profile (OBVIOUSLY AN ARTEFACT)
0h GeneA 3 reads
0h GeneA 2 reads
0h GeneA 0 reads
0h GeneA 1 reads
0h GeneA 3 reads
24h GeneA 0 reads
24h GeneA 1 reads
24h GeneA 2 reads
24h GeneA 0 reads
24h GeneA 1 reads
But DeSeq2 analysis of DE of these genes gives me a profile like this:
baseMean log2FoldChange lfcSE stat pvalue padj
31.88739159 -4.026822896 0.943450084 -4.268188603 1.97E-05 0.007173227
How do I filter for such artefacts ? Though I give an example here, my results are severely afflicted with these kind of low read count but highly significant statistics.
Any suggestion is highly appreciated...
I cannot set a minreadcount filter as these genes will have higher read count as the time line progresses (and will also skew the stats if I only remove it for one time point)