Question: edgeR & ERCC normalization
0
gravatar for moxu
2.8 years ago by
moxu440
moxu440 wrote:

edgeR requires the input of raw counts of RNA-seq WITHOUT ANY kind of normalization. But, it seems reasonable to me for the raw counts to be normalized by ERCC spike in, right? BTW, how do you do ERCC spike in normalization? And what's the algorithm to do the ERCC normalization?

Thank you!

rna-seq • 977 views
ADD COMMENTlink modified 2.8 years ago by geek_y9.6k • written 2.8 years ago by moxu440
1
gravatar for geek_y
2.8 years ago by
geek_y9.6k
Barcelona/CRG/London/Imperial
geek_y9.6k wrote:

RUVSeq

It does ERCC normalization and internally uses edgeR for differential expression analysis, which is exactly what you are looking for.

ADD COMMENTlink modified 2.8 years ago • written 2.8 years ago by geek_y9.6k

Do you mean edgeR can handle ERCC normalization internally? That sounds great.

Thank you!

ADD REPLYlink written 2.7 years ago by moxu440

BTW, I used RSEM to get the sequence count, and the output of RSEM is not integer but with decimal points such as 4.26, 1.91, etc. Will this affect the performance of edgeR?

Thanks a lot!

ADD REPLYlink written 2.7 years ago by moxu440
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