comparisson of RNA-seq FPKMs across samples
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5.6 years ago

Dear BioStars community,

I am trying to "recycle" some RNA-seq data published as supplementary material of the publication "High-throughput screening using patient-derived tumor xenografts to predict clinical trial drug response" but I am not sure if I can really use it for my purpose.

I have a matrix of fpkm values per gene for 376 samples. For each gene in each sample, I would like to know whether the gene in this sample is highly expressed compared to the whole population (e.g obtain a Z-score for the expression of the gene in the sample given the expression of this gene in the whole population).

I have read that fpkm values depend on the sequencing depth of each sample and, therefore, cannot be directly compared across samples. Is there a way to somehow transform fpkm values into something that could be compared across samples?

I have never worked with RNA-seq data so any contribution will be more than welcome, even if you think it is a simple and basic comment or suggestion. I am comfortable programming with Python but I can also use R, perl or command line tools.

Many thanks in advance,

LĂ­dia

RNA-Seq fpkm • 2.3k views
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4.0 years ago
FeiZhao • 0

You might as well try htseq-count and deseq2 to compare gene expression in different samples

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