[BioC] results interpretation

[Leonardo Pitombo [guest]]

Dear Dr. Michael,

I’m using DESeq2 to compare data from different treatments to find possible bioindicators. I applied the DESeq function by two ways:

A) treatmentdeseq <- phyloseq_to_deseq2(biom_otu_tax, ~treatment)

B) treatmentdeseq2<- phyloseq_to_deseq2(biom_otu_tax, ~treatment + condition x)

The intercept in both is the same, but the comparisons among treatments are (a bit) different when I call A and B. In B, does the condition exert some influence on analysis comparing treatments?
Could you explain why?

Thanks,
Leonardo M. Pitombo


 -- output of sessionInfo(): 

> sessionInfo("DESeq2")
R version 3.0.1 (2013-05-16)
Platform: x86_64-w64-mingw32/x64 (64-bit)

locale:
[1] LC_COLLATE=Dutch_Netherlands.1252  LC_CTYPE=Dutch_Netherlands.1252    LC_MONETARY=Dutch_Netherlands.1252
[4] LC_NUMERIC=C                       LC_TIME=Dutch_Netherlands.1252    

attached base packages:
character(0)

other attached packages:
[1] DESeq2_1.2.10

loaded via a namespace (and not attached):
 [1] ade4_1.6-2              annotate_1.40.0         AnnotationDbi_1.24.0    ape_3.0-11             
 [5] base_3.0.1              Biobase_2.22.0          BiocGenerics_0.8.0      biom_0.3.11            
 [9] Biostrings_2.30.1       cluster_1.14.4          codetools_0.2-8         colorspace_1.2-4       
[13] datasets_3.0.1          DBI_0.2-7               dichromat_2.0-0         digest_0.6.4           
[17] foreach_1.4.1           genefilter_1.44.0       GenomicRanges_1.14.4    ggplot2_0.9.3.1        
[21] glmmADMB_0.7.7          graphics_3.0.1          grDevices_3.0.1         grid_3.0.1             
[25] gtable_0.1.2            igraph_0.7.0            IRanges_1.20.6          iterators_1.0.6        
[29] labeling_0.2            lattice_0.20-24         locfit_1.5-9.1          MASS_7.3-29            
[33] Matrix_1.1-2            methods_3.0.1           multtest_2.18.0         MuMIn_1.9.13           
[37] munsell_0.4.2           nlme_3.1-113            parallel_3.0.1          permute_0.8-3          
[41] phyloseq_1.7.12         plyr_1.8                proto_0.3-10            R2admb_0.7.10          
[45] RColorBrewer_1.0-5      Rcpp_0.11.0             RcppArmadillo_0.4.000.2 reshape2_1.2.2         
[49] RJSONIO_1.0-3           RSQLite_0.11.4          scales_0.2.3            splines_3.0.1          
[53] stats_3.0.1             stats4_3.0.1            stringr_0.6.2           survival_2.37-7        
[57] tools_3.0.1             utils_3.0.1             vegan_2.0-10            XML_3.98-1.1           
[61] xtable_1.7-1            XVector_0.2.0      

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