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
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