Question: can we replace #N/a with 0 for using edgeR
0
gravatar for saumya.sharma1509
6 months ago by
saumya.sharma15090 wrote:

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

rna-seq R • 219 views
ADD COMMENTlink modified 6 months ago • written 6 months ago by saumya.sharma15090
1

Where does your count came from ?

ADD REPLYlink written 6 months ago by Bastien Hervé4.4k

we have fpkm values and obtained it from NCBI geoset

ADD REPLYlink written 6 months ago by saumya.sharma15090

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

ADD REPLYlink written 6 months ago by Bastien Hervé4.4k
2
gravatar for Benn
6 months ago by
Benn7.5k
Netherlands
Benn7.5k wrote:

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.

ADD COMMENTlink modified 6 months ago • written 6 months ago by Benn7.5k
1

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

C: FPKM not suitable for DE?

ADD REPLYlink written 6 months ago by Bastien Hervé4.4k
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