Folks,
We are looking at RNASeq data from rat brain.
The experimental protocol is to compare sham (or S: saline treated) versus experimental (or C: chemical treated).
Several pairs of animals were tested.
When I group all the data from groups 1, 2 & 3 the number of genes with significantly different expression ( ie with "yes" in *.diff from cuffdiff output) can be a few score of genes. However, when I look a the C vs S for a single pair I can see several thousand genes, isoforms splicing variants. Why the huge decrease? I tell the experimentalists that this may be due to the multiple test corrections but they are not convinced.
When I examine pairs separately ( ie group 1 C vs S, group 2 C vs S and group 3 C vs S) I get a number of significant genes and isoforms that show common expression patterns in all groups.
However the number of splicing events shows almost no instances where the same event is found in all three groups. Why is that?
Starr
We are looking at RNASeq data from rat brain.
The experimental protocol is to compare sham (or S: saline treated) versus experimental (or C: chemical treated).
Several pairs of animals were tested.
When I group all the data from groups 1, 2 & 3 the number of genes with significantly different expression ( ie with "yes" in *.diff from cuffdiff output) can be a few score of genes. However, when I look a the C vs S for a single pair I can see several thousand genes, isoforms splicing variants. Why the huge decrease? I tell the experimentalists that this may be due to the multiple test corrections but they are not convinced.
When I examine pairs separately ( ie group 1 C vs S, group 2 C vs S and group 3 C vs S) I get a number of significant genes and isoforms that show common expression patterns in all groups.
However the number of splicing events shows almost no instances where the same event is found in all three groups. Why is that?
Starr
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