Analyzing DEG from different dataset in my study design

Analyzing DEG from different dataset in my study design

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Hi
I have a situation here which make me confused and not sure if i have every thing right.

I compared 5 different datasets in one study with each other separately. for example data1 vs data2, data1 vs data3, data1 vs data4 and data1 vs data5.
Attention: All of those data were from healthy individuals which had different conditions.
The purpose was to find genes which have our expected condition in healthy individuals.
Then after gathering all results from above analysis we compared their readcounts with other cancer datasets(readcounts) from other studies.(All datasets in this study design were got from raw datas)

I got my result which seems already good.
But I don’t know in theory, my study design have any problem or not? specially the BOLD part.
PCA plots in this plot shows 95% variance which make me worry.

looking forward for any suggestions from experts
Kind regards.


RNA-Seq

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