NOIseq Probability column or Calculate P-value for each row

Question

[Pratibha kadam]

Hello There,

I am working with RNAseq data without replicates. for that reason to get differential expression of the genes I used R package NOIseq.

The tool has given the log2fold change and probability column which is probability of expression. I am not sure whether the probability column is same as p-value coz at high p-value it is having high expression. Usually I consider p-value (0.05) for Signiant genes.

If anyone has used this package please revert on selecting the significant expressed genes.

Otherwise I need to calculate p-value separately for each row.

Output from NOIseq:

Transcript id   IHF34   IHF34_A log2foldchange  IHF34-IHF34_A   prob    ranking
NR_001445.2 21749.39464 44.61359232 8.929276211 21704.78105 1   21704.78288
NR_004387.1 3413.156962 1.439148139 11.21167594 3411.717813 0.999999644 3411.736235
NR_145670.1 2840.505071 12.95233325 7.776791658 2827.552738 0.999999644 2827.563433
NR_003051.3 3269.04589  20.14807395 7.342083888 3248.897816 0.999999644 3248.906112
NM_001369451.1  2229.929215 5.037018488 8.790212173 2224.892196 0.999998932 2224.909561

I want to calculate p-value for IHF34(Control) and IHF34_A(Treated) column.

Please let me know how to calculate the p-value for each row in the dataset.

[kuttibiotech2009]

Hi Pratibha kadam,

I don't know weather I am saying it right or not. But, I have seen a bioinformatician while doing NOIseq. He has calculated P-Values using probability values, Example ; 1 - 0.950233632 (Prob) = 0.049766368 (P-Value)