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Greetings,
I have transcriptome data of benign, tumor and metastasis tissue from 4 patients. Additionally, I have two patients where I have only one and two samples, respectively. Can I combine them to improve coverage/significance of differential expression? Intiutively, I think since cancer is so diverse, I would need all three samples from a patient for "reference purposes". On the other hand, it hurts to completely throw away a couple of good sequencing runs, and the pipelines put the data together without knowing the identities of the patients.
I am using both edgeR and tophat-fusion/cufflinks pipeline.
Seems like a very basic kind of question, sorry if already answered or too obvious.
I have transcriptome data of benign, tumor and metastasis tissue from 4 patients. Additionally, I have two patients where I have only one and two samples, respectively. Can I combine them to improve coverage/significance of differential expression? Intiutively, I think since cancer is so diverse, I would need all three samples from a patient for "reference purposes". On the other hand, it hurts to completely throw away a couple of good sequencing runs, and the pipelines put the data together without knowing the identities of the patients.
I am using both edgeR and tophat-fusion/cufflinks pipeline.
Seems like a very basic kind of question, sorry if already answered or too obvious.