[BioC] time course differential analysis - design matrix

Fri Mar 28 14:41:04 CET 2014

Hi Agata,

On 3/28/2014 5:18 AM, Agata [guest] wrote:
> Dear all,
>
> I am doing differential expression analysis and I have a question concerning time course experiments (Single-Channel Experimental Designs).
>
> I have one cell line that was treated in 4 different ways. I want to check which genes respond dierently over time for different treatments. I did 4 different comparisons.
>
> I have treatment A, B, C and D, and I compared groups: A-B, A-C, C-D and B-D. For all my data I created ONE design matrix, and FOUR contrast.diff.matrices. For the fit() function I have used the esetPROC with all my data. This was followed by contrast.fit() and eBayes() functions. At the end I got top differentially expressed genes (from topTableF() function).
>
> Additionally, I did almost the same thing, but I created FOUR different design matrices and FOUR contrast.diff.matrices for all my comparisons. I extracted the subset of esetPROC only with the data I needed for the comparison, and continued as described above.
>
> I got different results for those two approaches. The adj.p.values were much smaller for the first approach than for the second one. I assume it is because of the eBayes function. Could you please explain me which approach is the correct/better one and why?

It's a combination of the eBayes function and the fact that you estimate 
gene-wise variances using all the data, rather than a subset (in the 
first analysis, that is).

Both methods are technically correct, but as you have already noted, the 
first method is more powerful, so in my mind it is to be preferred.

Best,

Jim

>
> Best wishes,
> Agata
>
>
>
>   -- output of sessionInfo():
>
> R version 3.0.2 (2013-09-25)
> Platform: x86_64-unknown-linux-gnu (64-bit)
>
> locale:
> [1] C
>
> attached base packages:
> [1] parallel  stats     graphics  grDevices utils     datasets  methods
> [8] base
>
> other attached packages:
>   [1] gplots_2.12.1            lattice_0.20-24          sva_3.8.0
>   [4] mgcv_1.7-26              nlme_3.1-111             corpcor_1.6.6
>   [7] vsn_3.30.0               marray_1.40.0            hgug4112a.db_2.10.1
> [10] org.Hs.eg.db_2.10.1      Agi4x44PreProcess_1.22.0 genefilter_1.44.0
> [13] annotate_1.40.0          AgiMicroRna_2.12.0       affycoretools_1.34.0
> [16] KEGG.db_2.10.1           GO.db_2.10.1             RSQLite_0.11.4
> [19] DBI_0.2-7                AnnotationDbi_1.24.0     preprocessCore_1.24.0
> [22] affy_1.40.0              Biobase_2.22.0           BiocGenerics_0.8.0
> [25] biomaRt_2.18.0           limma_3.18.12            WriteXLS_3.4.0
>
> loaded via a namespace (and not attached):
>   [1] AnnotationForge_1.4.4    BSgenome_1.30.0          BiocInstaller_1.12.0
>   [4] Biostrings_2.30.1        Category_2.28.0          DESeq2_1.2.10
>   [7] Formula_1.1-1            GOstats_2.28.0           GSEABase_1.24.0
> [10] GenomicFeatures_1.14.2   GenomicRanges_1.14.4     Hmisc_3.14-0
> [13] IRanges_1.20.6           KernSmooth_2.23-10       MASS_7.3-29
> [16] Matrix_1.1-2             PFAM.db_2.10.1           R.methodsS3_1.6.1
> [19] R.oo_1.17.0              R.utils_1.29.8           R2HTML_2.2.1
> [22] RBGL_1.38.0              RColorBrewer_1.0-5       RCurl_1.95-4.1
> [25] Rcpp_0.11.0              RcppArmadillo_0.4.000.2  ReportingTools_2.2.0
> [28] Rsamtools_1.14.3         VariantAnnotation_1.8.12 XML_3.98-1.1
> [31] XVector_0.2.0            affyio_1.30.0            annaffy_1.34.0
> [34] biovizBase_1.10.7        bit_1.1-11               bitops_1.0-6
> [37] caTools_1.16             cluster_1.14.4           codetools_0.2-8
> [40] colorspace_1.2-4         dichromat_2.0-0          digest_0.6.4
> [43] edgeR_3.4.2              ff_2.2-12                foreach_1.4.1
> [46] gcrma_2.34.0             gdata_2.13.2             ggbio_1.10.11
> [49] ggplot2_0.9.3.1          graph_1.40.1             grid_3.0.2
> [52] gridExtra_0.9.1          gtable_0.1.2             gtools_3.3.0
> [55] hwriter_1.3              iterators_1.0.6          labeling_0.2
> [58] latticeExtra_0.6-26      locfit_1.5-9.1           munsell_0.4.2
> [61] oligoClasses_1.24.0      plyr_1.8                 proto_0.3-10
> [64] reshape2_1.2.2           rtracklayer_1.22.3       scales_0.2.3
> [67] splines_3.0.2            stats4_3.0.2             stringr_0.6.2
> [70] survival_2.37-7          tools_3.0.2              xtable_1.7-1
> [73] zlibbioc_1.8.0
>
>
> packageDescription('limma')$Maintainer
> [1] "Gordon Smyth <smyth at wehi.edu.au>"
>
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>
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-- 
James W. MacDonald, M.S.
Biostatistician
University of Washington
Environmental and Occupational Health Sciences
4225 Roosevelt Way NE, # 100
Seattle WA 98105-6099