Hi I am trying to run the command cumNorm().
When I go through the tutorial I get an output and when I run the command on simulated data it works as well. However, when I try to run the command on my real data the output is a bunch of NAs.
Any suggestions?
> obj<-newMRexperiment(otu_table_final)
> cumNorm(obj)
MRexperiment (storageMode: environment)
assayData: 57394 features, 255 samples
element names: counts
protocolData: none
phenoData: none
featureData: none
experimentData: use 'experimentData(object)'
Annotation:
Warning message:
In cumNormStatFast(obj) : Low quantile estimate. Default value being used.
> head(normFactors(obj))
X02.HA.Forehead.375338 X02.HA.Stool.374811
NA NA
X02.HB.Forehead.374920 X02.HB.Stool.375396
NA NA
X02.HC.Forehead.375061 X02.HC.Stool.374906
NA NA
That shouldn't be a problem,
Feel free to send me a MRE (minimally reproducible example) or your dataset privately and I'll take a look at the specific issue for you
https://www.dropbox.com/s/k6phpcdfxsni0bg/otu_table_final.csv?dl=0
Thank you!!
Work for you?