Question

metagenomeSeq - normFactors

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Brian Smith ▴ 120

@brian-smith-6197

Last seen 5.1 years ago

United States

Hi,

I was trying to get the normalization factors with the example in the package metagenomeSeq. I get all NAs! What am I doing wrong?

code and output:

===============

> data(lungData)

> head(normFactors(lungData))
[,1]
CHK_6467_E3B11_BRONCH2_PREWASH_V1V2 NA
CHK_6467_E3B11_OW_V1V2 NA
CHK_6467_E3B08_OW_V1V2 NA
CHK_6467_E3B07_BAL_A_V1V2 NA
CHK_6467_E3B11_BAL_A_V1V2 NA
CHK_6467_E3B09_OP_V1V2 NA

My sessionInfo():

> sessionInfo()
R version 3.2.2 (2015-08-14)
Platform: x86_64-apple-darwin13.4.0 (64-bit)
Running under: OS X 10.10.1 (Yosemite)

locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

attached base packages:
[1] grid stats4 parallel stats graphics grDevices utils datasets methods base

other attached packages:
[1] tsne_0.1-2 ggplot2_1.0.1 fossil_0.3.7 shapefiles_0.7 foreign_0.8-66 maps_3.0.0-2
[7] sp_1.2-1 pheatmap_1.0.7 plyr_1.8.3 ape_3.3 vegan_2.3-1 lattice_0.20-33
[13] permute_0.8-4 phyloseq_1.14.0 edgeR_3.12.0 DESeq2_1.10.0 RcppArmadillo_0.6.200.2.0 Rcpp_0.12.1
[19] SummarizedExperiment_1.0.0 GenomicRanges_1.22.0 GenomeInfoDb_1.6.0 IRanges_2.4.1 S4Vectors_0.8.0 metagenomeSeq_1.12.0
[25] RColorBrewer_1.1-2 glmnet_2.0-2 foreach_1.4.3 Matrix_1.2-2 limma_3.26.1 Biobase_2.30.0
[31] BiocGenerics_0.16.0 XML_3.98-1.3

loaded via a namespace (and not attached):
[1] splines_3.2.2 gtools_3.5.0 Formula_1.2-1 latticeExtra_0.6-26 RSQLite_1.0.0 chron_2.3-47 digest_0.6.8
[8] XVector_0.10.0 colorspace_1.2-6 genefilter_1.52.0 zlibbioc_1.16.0 xtable_1.8-0 scales_0.3.0 gdata_2.17.0
[15] BiocParallel_1.4.0 annotate_1.48.0 mgcv_1.8-9 nnet_7.3-11 proto_0.3-10 survival_2.38-3 RJSONIO_1.3-0
[22] magrittr_1.5 nlme_3.1-122 MASS_7.3-44 gplots_2.17.0 tools_3.2.2 data.table_1.9.6 matrixStats_0.15.0
[29] stringr_1.0.0 munsell_0.4.2 locfit_1.5-9.1 cluster_2.0.3 AnnotationDbi_1.32.0 lambda.r_1.1.7 Biostrings_2.38.0
[36] compiler_3.2.2 ade4_1.7-2 caTools_1.17.1 futile.logger_1.4.1 iterators_1.0.8 biom_0.3.12 igraph_1.0.1
[43] labeling_0.3 bitops_1.0-6 gtable_0.1.2 codetools_0.2-14 multtest_2.26.0 DBI_0.3.1 reshape2_1.4.1
[50] gridExtra_2.0.0 Hmisc_3.17-0 futile.options_1.0.0 KernSmooth_2.23-15 stringi_1.0-1 geneplotter_1.48.0 rpart_4.1-10
[57] acepack_1.3-3.3

metagenomeseq • 1.5k views

ADD COMMENT • link updated 10.0 years ago by Joseph Nathaniel Paulson ▴ 280 • written 10.0 years ago by Brian Smith ▴ 120

score 1 · Answer 1 · 2015-11-13

Hey - You have to normalize the dataset first! > head(normFactors(cumNorm(lungData))) CHK_6467_E3B11_BRONCH2_PREWASH_V1V2 CHK_6467_E3B11_OW_V1V2 67 2475 CHK_6467_E3B08_OW_V1V2 CHK_6467_E3B07_BAL_A_V1V2 2198 836 CHK_6467_E3B11_BAL_A_V1V2 CHK_6467_E3B09_OP_V1V2 1008 1820 On Fri, Nov 13, 2015 at 12:35 PM Brian Smith [bioc] < noreply@bioconductor.org> wrote: > Activity on a post you are following on support.bioconductor.org > > User Brian Smith <https: support.bioconductor.org="" u="" 6197=""/> wrote Question: > metagenomeSeq - normFactors <https: support.bioconductor.org="" p="" 74544=""/>: > > Hi, > > I was trying to get the normalization factors with the example in the > package metagenomeSeq. I get all NAs! What am I doing wrong? > > code and output: > > =============== > > > data(lungData) > > > head(normFactors(lungData)) > [,1] > CHK_6467_E3B11_BRONCH2_PREWASH_V1V2 NA > CHK_6467_E3B11_OW_V1V2 NA > CHK_6467_E3B08_OW_V1V2 NA > CHK_6467_E3B07_BAL_A_V1V2 NA > CHK_6467_E3B11_BAL_A_V1V2 NA > CHK_6467_E3B09_OP_V1V2 NA > > > > My sessionInfo(): > > > sessionInfo() > R version 3.2.2 (2015-08-14) > Platform: x86_64-apple-darwin13.4.0 (64-bit) > Running under: OS X 10.10.1 (Yosemite) > > locale: > [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8 > > attached base packages: > [1] grid stats4 parallel stats graphics grDevices utils > datasets methods base > > other attached packages: > [1] tsne_0.1-2 ggplot2_1.0.1 fossil_0.3.7 > shapefiles_0.7 foreign_0.8-66 > maps_3.0.0-2 > [7] sp_1.2-1 pheatmap_1.0.7 plyr_1.8.3 > ape_3.3 vegan_2.3-1 > lattice_0.20-33 > [13] permute_0.8-4 phyloseq_1.14.0 edgeR_3.12.0 > DESeq2_1.10.0 RcppArmadillo_0.6.200.2.0 > Rcpp_0.12.1 > [19] SummarizedExperiment_1.0.0 GenomicRanges_1.22.0 > GenomeInfoDb_1.6.0 IRanges_2.4.1 S4Vectors_0.8.0 > metagenomeSeq_1.12.0 > [25] RColorBrewer_1.1-2 glmnet_2.0-2 foreach_1.4.3 > Matrix_1.2-2 limma_3.26.1 > Biobase_2.30.0 > [31] BiocGenerics_0.16.0 XML_3.98-1.3 > > loaded via a namespace (and not attached): > [1] splines_3.2.2 gtools_3.5.0 Formula_1.2-1 > latticeExtra_0.6-26 RSQLite_1.0.0 chron_2.3-47 > digest_0.6.8 > [8] XVector_0.10.0 colorspace_1.2-6 genefilter_1.52.0 > zlibbioc_1.16.0 xtable_1.8-0 scales_0.3.0 > gdata_2.17.0 > [15] BiocParallel_1.4.0 annotate_1.48.0 mgcv_1.8-9 > nnet_7.3-11 proto_0.3-10 survival_2.38-3 > RJSONIO_1.3-0 > [22] magrittr_1.5 nlme_3.1-122 MASS_7.3-44 > gplots_2.17.0 tools_3.2.2 data.table_1.9.6 > matrixStats_0.15.0 > [29] stringr_1.0.0 munsell_0.4.2 locfit_1.5-9.1 > cluster_2.0.3 AnnotationDbi_1.32.0 lambda.r_1.1.7 > Biostrings_2.38.0 > [36] compiler_3.2.2 ade4_1.7-2 caTools_1.17.1 > futile.logger_1.4.1 iterators_1.0.8 biom_0.3.12 igraph_1.0.1 > > [43] labeling_0.3 bitops_1.0-6 gtable_0.1.2 > codetools_0.2-14 multtest_2.26.0 DBI_0.3.1 > reshape2_1.4.1 > [50] gridExtra_2.0.0 Hmisc_3.17-0 futile.options_1.0.0 > KernSmooth_2.23-15 stringi_1.0-1 geneplotter_1.48.0 rpart_4.1-10 > > [57] acepack_1.3-3.3 > ------------------------------ > > Post tags: metagenomeseq > > You may reply via email or visit metagenomeSeq - normFactors >