FoldChange calculation for two samples

[bvk]

Hi all,

I have two RNA-Seq samples. Detecting differential expressed genes for two samples is not possible. So, I want to calculate fold change for Sample1 vs Sample2.

Based on that I want to detect differential expressed genes.

Each sample has the following information.

tracking_id, class_code, nearest_ref_id, gene_id, gene_short_name, tss_id, locus length, coverage, FPKM, FPKM_conf_lo, FPKM_conf_hi, FPKM_status

Is there any R package to calculate FC for two smaples?

[SamCurt]

I don't understand what you mean here. While you understand "detecting differential expressed genes for two samples is not possible" without biological replicates, how do you "based on [fold change] ... detect differential expressed genes"?

With that kind of data the best I can do is FPKM1/FPKM2, and that's it.

[fahmida]

Agree with SamCurt. You can quantify the expression level of genes for two samples, however, you do not have any statistical power to reliably estimate the differential expression.

[Michael.Ante]

I also have to agree. You can have a look at GFOLD. It is not calling a test for differential expression but rather computes a "more reliable" fold-change.

For further experiments I'd suggest to plan the design in order to satisfy the statistical requirements.