**0**wrote:

Hi,

I was trying to visualize the normalized count of my data, however, I was running into errors:

normalized.count <- as.data.frame(counts(DESeq2, normalized=TRUE))

Error in as.data.frame(counts(DESeq2, normalized = TRUE)) :

error in evaluating the argument 'x' in selecting a method for function 'as.data.frame': Error in .local(object, ...) :

first calculate size factors, add normalizationFactors, or set normalized=FALSE

I was following DESeq2 vignette, whenever I put "normalized=TRUE", like

select<-order(rowMeans(counts(DESeq2, normalized=TRUE)), decreasing=TRUE)[1:30]

Error in .local(object, ...) :

first calculate size factors, add normalizationFactors, or set normalized=FALSE.

But how do I add normalizationFactors?

Also when I ran plot Dispersion Estimates, the following error message is shown:

plotDispEsts(DESeq2)

Error in plot.window(...) : need finite 'xlim' values

In addition: Warning messages:

1: In min(py[py > 0], na.rm = TRUE) :

no non-missing arguments to min; returning Inf

2: In is.na(x) : is.na() applied to non-(list or vector) of type 'NULL'

3: In min(x) : no non-missing arguments to min; returning Inf

4: In max(x) : no non-missing arguments to max; returning -Inf

5: In min(x) : no non-missing arguments to min; returning Inf

6: In max(x) : no non-missing arguments to max; returning -Inf

If anyone knows how to solve the problem?

Thanks a lot!

**15k**• written 2.4 years ago by yuan.qing •

**0**