Question: Rank Genes By FPKM for only One Sample
0
gravatar for Ron
4.5 years ago by
Ron930
United States
Ron930 wrote:

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

ADD COMMENTlink modified 4.5 years ago by David Fredman980 • written 4.5 years ago by Ron930
1
gravatar for Gjain
4.5 years ago by
Gjain5.3k
Göttingen, Germany
Gjain5.3k wrote:

Please check this blogpost. This should clear your doubts. 

ADD COMMENTlink written 4.5 years ago by Gjain5.3k

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

ADD REPLYlink written 4.5 years ago by Ron930

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).

ADD REPLYlink modified 4.5 years ago • written 4.5 years ago by David Fredman980

yes that should be enough. 

ADD REPLYlink written 4.5 years ago by Gjain5.3k

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.

ADD REPLYlink written 4.4 years ago by Ron930
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 857 users visited in the last hour