how to calculate the foldchange and p-value from a gene expression data?

Question

[khalilzoro26]

I have a file like this,two groups and three samples each group:

M1  M2  M3  S1  S2  S3
 AABR07013255.1 -13.22297234    -8.888415999    -8.517115219    -12.7680452 -10.51570246 -9.996496728
Gad1    -12.92777691    -14.41343841    -11.9724142 -12.47175352    -15.11984846    -33.80671378
Alx4    -12.58264741    -11.49120972    -11.43475629    -33.80671378    -33.80671378    -13.35749508
Tmco5b  -12.15345006    -33.80671378    -33.80671378    -33.80671378    -12.76876909    -33.80671378
Cbln1   -12.13320598    -13.03636228    -11.2634888 -33.80671378    -14.74161303    -13.90953426
Tcf15   -4.191269729    -5.08277309 -5.907450216    -4.477222532    -4.848447553    -4.73038896
Steap1  -33.80671378    -11.37580867    -9.211840196    -12.58985901    -9.491027535    -9.357845499

NOW, how can I calculate the foldchange and p-value of each gene like and get the file like this:

Log2Foldchange  pvalue
RGD1304622  -1.139  1.37E-02
Slc26a1 -2.078  4.05E-02
Cdo1    -1.668  3.09E-03
Alas2   -2.078  6.10E-03
Gatm    -1.057  1.84E-02
Scarf2  -1.52   4.61E-02
Ros1    1.698   2.62E-02
Cfb -1.346  3.13E-02

Thank you very much!I'm a beginner!

[Devon Ryan]

What do the values in the original matrix actually represent? BTW, the general answer to this is to use DESeq2/edgeR/limma in R, but you can't with the input you have.

[khalilzoro26]

the original matrix is from the Normalization Analysis that I use the OMICSBEAN website. I upload the original data to the OMICSBEAN like this:

   gene symbol  M1  M2  M3  S1  S2  S3
   AABR07013255.1   0.108742    1.42499 1.88208 0.169047    0.541435    0.975147
   Gad1 0.133432    0.0309467   0.171589    0.207587    0.0222618   0
   Alx4 0.169494    0.234581    0.249081    0   0   0.0949093
   Tmco5b   0.228221    0   0   0   0.113581    0
   Cbln1    0.231446    0.0803814   0.280477    0   0.0289348   0.0647334
   Tcf15    56.9129 19.9262 11.4875 52.9412 27.5144 37.5255
   Steap1   0   0.254116    1.1628  0.19127 1.10155 1.51818

the data is from the FPKM ,you mean I should use this data to calculate the foldchange in R?

[Devon Ryan]

Delete the results from "omicsbean", they are of no use to anyone. Can you access the raw data from which the FPKMs were derived? As a general rule, FPKMs should not be used for statistics.

[khalilzoro26]

So what data should I use to calculate it?

[Devon Ryan]

Ideally raw counts.