Hi,
I'm looking for the quality control test of RNA-seq gene expression data. I have just expression values, not the sequence. which kind of test I can think of about it to have feeling about the quality of data?
I found the similar thing for microarray gene expression data.http://res.illumina.com/documents/products/technotes/technote_gene_expression_data_quality_control.pdf
If you have several biological replicates - build scatterplots among them and compute correlation. You can also consider analyzing gene expression value distribution for "abnormalities" (e.g. with Q-Q plot), in this case you need some sample that is made using relatively same techniques and use the same expression value calculation scheme (i.e. TopHat -> FPKM -> log10).
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mikhail.shugay
A PCA or hierarchical clustering are pretty much your only options.
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Devon Ryan
Is a correlation plot generated between biological replicates would not be enough?
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GouthamAtla
If you have a lot of samples, then the correlation plots end up getting rather large and difficult to interpret, that's when PCA plots and such become a bit simpler.
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Devon Ryan
It'll tell you about the underlying variance structure. If you have samples clustering in odd ways, then there are likely batch effects on sets of genes.
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Devon Ryan
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