metagenomeSeq: cumNormStat normalization default
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Brian Smith ▴ 120
@brian-smith-6197
Last seen 10 months ago
United States

Hi,

I was trying to normalize my count/reads data using cumNormStat function. The code executes with the 'default value', and doesn't appear to change the count values after the normalization. Am I doing something wrong? Or is the 'default value' the most appropriate value for my dataset?

 

> p=cumNormStat(mrobj) # calculateNormFactors
Default value being used.
>     mrobj2 = cumNorm(mrobj,p=p) # Normalize


>     print(MRcounts(mrobj)[1:3,1:3])
         sample_1 sample_10 sample_100
Otu00001     4957       169          1
Otu00002      869      3604          0
Otu00003      425      1368          0
>     print(MRcounts(mrobj2)[1:3,1:3])
         sample_1 sample_10 sample_100
Otu00001     4957       169          1
Otu00002      869      3604          0
Otu00003      425      1368          0

 

thanks!!

metagenomeseq microbiome • 835 views
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@joseph-nathaniel-paulson-6442
Last seen 4.3 years ago
United States

Hi Brian,

Please see the options for `MRcounts`. There are flags to return the normalized values.

 

 

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Brian Smith ▴ 120
@brian-smith-6197
Last seen 10 months ago
United States

Hi Joseph,

Thanks! That worked. Sorry for very basic questions - just got started on microbiome.

I used silva and mothur to get my OTUs. However, I get something like :

=========

> yy <- aggTax(myobj, lvl = "phylum", out = "MRexperiment")
> MRcounts(yy)[1:5,1:5]

sample_4 sample_5 sample_6 sample_7 sample_11
Actinobacteria 159 714 769 910 387
Actinobacteria(85) 0 0 0 0 0
Bacteria_unclassified 0 49 24 29 202
Bacteria_unclassified(90) 0 0 0 0 0
Bacteria_unclassified(95) 0 0 0 0 0

===========

Is there a function that would aggregate/collapse these so that all the Bacteria are in a single row, all the Actinobacteria in another row etc.

 

many thanks!

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