I am very interested in using metagenomeSeq. I have pretty much copied (verbatim) the instructions in the manual (up to page 11) into an R script. Unfortunately, it produces different results from the one depicted in the manual (namely it does not estimate normalization factors, such result is below:

                                              Subjec Scaling.fac or.Quan

1 CHK_6467_E3B11_BRONCH2_PREWASH_V1V2\tNA\t2\t60\t271          NA      NA

2           CHK_6467_E3B11_OW_V1V2\tNA\t1\t3299\t7863          NA      NA

3           CHK_6467_E3B08_OW_V1V2\tNA\t1\t2994\t8360          NA      NA

4        CHK_6467_E3B07_BAL_A_V1V2\tNA\t1\t1188\t5249          NA      NA

5        CHK_6467_E3B11_BAL_A_V1V2\tNA\t1\t1098\t3383          NA      NA

  ile.value.Number.of.iden ified.fea ures.Library.size

1                       NA        NA                NA

2                       NA        NA                NA

3                       NA        NA                NA

4                       NA        NA                NA

5                       NA        NA                NA

Thank you Juan for your interest in metagenomeSeq.

The easiest way to make sure you're not copying incorrectly the code is to enter:

browseVignettes("metagenomeSeq")

This will produce a site you can view the pdf, source code, and Rscript because the vignette is directly produced when installed. 

Similar to what is on the Bioconductor page (see Rscript) and here. Sometimes copying directly from a PDF document fails. If you run the code chunks, including code chunk number 20 below, you should see that it worked.

###################################################
### code chunk number 20: exportStats
###################################################
exportStats(lungData[,1:5],file=file.path(dataDirectory,"tmp.tsv"))
head(read.csv(file=file.path(dataDirectory,"tmp.tsv"),sep="\t"))