Hello, I'm a student.
I have an expression matrix of 1208 samples (1095 tumor and 113 normal) downloaded from TCGA (RNA-Seq) and I have to adjust for batch effects. http://bioinformatics.mdanderson.org/tcgambatch/ suggests that there are 3 batches: type(tumor/normal), plateId and TSS but in a different forum, a boy said me that he has never noticed these batch effects.
So I'm a bit confused...
Is there anyone who can explain me how to find batch effects? I know that I can look for them with PCA but I have no idea how to interpret the graph. Can I consider tumor and normal as batch effects?
Thanks in advance
I have an expression matrix of 1208 samples (1095 tumor and 113 normal) downloaded from TCGA (RNA-Seq) and I have to adjust for batch effects. http://bioinformatics.mdanderson.org/tcgambatch/ suggests that there are 3 batches: type(tumor/normal), plateId and TSS but in a different forum, a boy said me that he has never noticed these batch effects.
So I'm a bit confused...
Is there anyone who can explain me how to find batch effects? I know that I can look for them with PCA but I have no idea how to interpret the graph. Can I consider tumor and normal as batch effects?
Thanks in advance
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