Rank Genes By FPKM for only One Sample

Question

[Ron]

Hey everyone,

I know that we can use FPKM's for further downstream analysis with cuffdiff and bioconductor packages when we have multiple samples.But if we have FPKM's for a SINGLE sample and want to rank top expressed genes and give them ranks,is there any method to do that? I think we have to do some normalization as well.

Best,
Ron

Answer 1

[Gjain]

Please check this blogpost. This should clear your doubts.

[Ron]

Nice.Thats helpful to understand more on FPKMS and normalization.How should I proceed on ranking those genes by FPKM's

[David Fredman]

No further normalization is required to compare the expression of genes within one sample.Just sort (rank) your genes by their FPKM or TPM values. You can do this in Excel (!), the *nix command line, or any programming language (including R). Those with the highest values are most abundant transcripts in the sample (barring any missing or incorrect gene annotation).

[Gjain]

Yes that should be enough.

[Ron]

Also, in RNASeq do we want to look at the low expressed genes? In this scenario,I am removing the genes with 0 FPKM's and looking at the low values.