Hi all,
I am trying to run DE analysis on miRNAs samples (from two conditions).
In a recently published article it was mentioned that "TMM" normalization method is the least suitable to miRNAs and they suggested to use quantile normalization.
I tried to change the method parameter to "upperquantile"
y <- calcNormFactors(y,method="upperquartile")
What I was getting when running the next step is:
y <- estimateCommonDisp(y) # Estimates common dispersion
Error in if (mx < tol) { : missing value where TRUE/FALSE needed
When looking at the y variable I have noticed that all of the norm.factors are NaN.
Worth mentioning that I didn't have this problem when running the "TMM" and "RLE" normalization methods.
My questions:
1. What might cause the problem when running "upperquantile" normalization in EdgeR?
2. How can I use the "quantile" normalization and not the "upperquantile"? Change the Percentile some how? (p parameter)
3.From the manual I noticed that the "RLE" normalization is similar to the implemented normalization in DEseq , but when running EdgeR with "RLE" vs DEseq I have been getting very different results ? Why is that?
I will appreciate your answers,
Thanks,
Moriah
I am trying to run DE analysis on miRNAs samples (from two conditions).
In a recently published article it was mentioned that "TMM" normalization method is the least suitable to miRNAs and they suggested to use quantile normalization.
I tried to change the method parameter to "upperquantile"
y <- calcNormFactors(y,method="upperquartile")
What I was getting when running the next step is:
y <- estimateCommonDisp(y) # Estimates common dispersion
Error in if (mx < tol) { : missing value where TRUE/FALSE needed
When looking at the y variable I have noticed that all of the norm.factors are NaN.
Worth mentioning that I didn't have this problem when running the "TMM" and "RLE" normalization methods.
My questions:
1. What might cause the problem when running "upperquantile" normalization in EdgeR?
2. How can I use the "quantile" normalization and not the "upperquantile"? Change the Percentile some how? (p parameter)
3.From the manual I noticed that the "RLE" normalization is similar to the implemented normalization in DEseq , but when running EdgeR with "RLE" vs DEseq I have been getting very different results ? Why is that?
I will appreciate your answers,
Thanks,
Moriah
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