can we replace #N/a with 0 for using edgeR

Question

[saumya.sharma1509]

hey I want to know that can I replace #N/A with the 0.it is an RNAseq data and I want to do the differential expression analysis in edgeR.
can I replace #N/A with 0

[Bastien Hervé]

Where does your count came from ?

[saumya.sharma1509]

we have fpkm values and obtained it from NCBI geoset

[Bastien Hervé]

Please, use to add reply grey button below my comment to keep this thread well indent and much more readable

As the NA value stand for : "I did not find this feature in your data" while 0 value stand for : "I have found this feature in your data but I counted 0 read on it".

If the feature is not measured, you can set the count to 0

Answer 1

[Benn]

edgeR is not suitable for analysis with FPKM, see user's guide section 2.3 on page 12.

Note that edgeR is designed to work with actual read counts. We not recommend that predicted transcript abundances are input the edgeR in place of actual counts.

[Bastien Hervé]

Ah yeah right too, I never used edgeR, but see also Kevin Blighe 's comment here about FPKM :

C: FPKM not suitable for DE?