Question: TCGA RNAseqV2 data matrix batch effect control and remove
gravatar for fractal61
3.9 years ago by
fractal610 wrote:

I have a RNAseqV2 data matrix, rows are genes and columns are samples and cells values are raw counts. I also have normlized data. Dimensions of data 18323 x 600. How can i check batch effect from this data and remove? Is it necessary process for obtaining differential expressed genes.

batch effect rna-seq • 1.4k views
ADD COMMENTlink modified 3.9 years ago by andrew.j.skelton736.0k • written 3.9 years ago by fractal610
gravatar for andrew.j.skelton73
3.9 years ago by
andrew.j.skelton736.0k wrote:

Use principle components analysis (PCA) to try and eyeball potential batch variables - You could also look at the SVA package too. Correcting for batch effects depends on the situation, but I'd advise adding the variable in as an additive term in the linear model design. See limma

ADD COMMENTlink written 3.9 years ago by andrew.j.skelton736.0k
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