So, the problem is that DESeq2 takes the average of FCs for each replicate and then converts the averaged FC into Log2. That means it considers FCs. Now to represent I need error bars. For error bars, I need Standard deviation. For standard deviation I need either FC or Log2Fc values for each replicate. I found that the Log2FC formed from individual Log2FCs is not equal to Log2FC from average of the FCs. (Which is how DESeq2 does it)

Now, if I represent avg (Log2FC) with error bars, this will be similar but not the same as calculated by DESeq2. For example, a log2 value calculated from avg (FCs)= -2.30 And log2 value calculated by doing avg(log2FCs) of the same data gives = -3.94 It seems, there is a significant difference in this case. Elsewise, I have to make a graph using FCs in y axis for a data which enlists DEGs in log form.

Abbreviations:

Avg= average

Can you please suggest a correct way to represent my data?

The standard error is readily calculated for you in the

`results()`

output in column`lfcSE`

. See`?results()`

as well as:https://support.bioconductor.org/p/93559/#93561

https://support.bioconductor.org/p/65318/

https://support.bioconductor.org/p/117348/

https://bioc.ism.ac.jp/packages/2.14/bioc/vignettes/DESeq2/inst/doc/beginner.pdf

From the latter:

Loved it! Thanks.