differenrially expressed mRNA pvalue FRD

Question

[yueli7]

Hi,

I have two transcriptomes mRNA samples which already have their FPKM value. Want to find their differentially expressed mRNA.

How can I calculate their p value and FDR value?

Any suggestions?

Thanks in advance for great help!

Yue

The file format:

Transcript ID    A_FPKM    B_FPKM
NV31142-RA    0    0
NV11327-RA    42.8691    38.1509
NV23694-RA    50.6658    18.4023
NV11424-RA    3.54337    1.06407
NV11484-RA    2.39216    0.898644
NV23739-RA    1.37778    75.791
NV11504-RA    8.72394    20.1218
NV11534-RA    3.45778    63.8315
NV11576-RA    0.584337    0.123136
NV24454-RA    9.70117    0.823623
NV24456-RA    8.58452    6.12176
NV24436-RA    5.20422    0.35093
NV11763-RA    2.79888    0.35609

[yueli7]

Thanks.

Thanks everyone for great help!

Answer 1

[mehran.karimzade]

If you have only one sample per group, it is not possible to calculate any p-value. For calculating p-value, you need a few samples per group to create a statistical model to evaluate the differential distribution of your FPKM values across the two groups.

For differential expression analysis on RNAseq measures such as FPKM, you can use edgeR or DESeq bioconductor package after reading their documentation that has extensive details and examples:

http://bioconductor.org/packages/release/bioc/html/edgeR.html

Answer 2

[andrew]

Mehran is correct. Usually a minimum of 3 samples per phenotype are required - so 6 samples in your case.