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  • Ahmadiut
    Junior Member
    • May 2015
    • 3
    #1

    TPM and FPLM problem?

    Hi
    I have used Illumina hiseq 2000 to sequence two samples (two organs of a plant) without replication. I know that without replication I can not deferentially analyze my data and I just want to report the gene expression of each sample (their TPM). The problem is: in one of my sample TPM value of all genes is more than their FPKM and in the other one FPKM>TPM. Is there any problem with my data?
    I think my data needs more normalization because TPM values of genes in one of my sample is greater than the other one in most cases.

    Example:
    Sample1
    Genes TPM FPKM
    gene1 20 15
    gene2 100 85
    gene3 250 195

    sample2
    Genes TPM FPKM
    gene1 5 7
    gene2 12 20
    gene3 35 40

    Any help will be appreciated,
    Thanks
    Last edited by Ahmadiut; 06-24-2016, 04:08 AM.
    Tags: differential analysis, normalization, rna-seq, rsem
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