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Hello BioC forum,
I am making a design matrix for gene expression data analysis with
the adjustment of Sex variable. The R code I am using is below. I
want to make sure if I am doing correctly. Thanks for your review and
feedback.
> library(limma)
> Sample<-factor(pd$Sample_Group, levels=c("Control","Case")) ###
treatment
> Sex<-factor(pd$Sex, levels=c("M","F")) ###
Sex
> design<-model.matrix(~Sample+Sex)
> design
(Intercept) SampleCase SexF
1 1 0 0
2 1 0 0
3 1 0 0
4 1 0 1
5 1 0 1
6 1 0 1
7 1 1 1
8 1 0 0
9 1 0 1
10 1 1 0
11 1 1 1
12 1 0 1
13 1 0 1
14 1 1 0
15 1 0 0
16 1 1 1
17 1 0 0
18 1 0 0
19 1 1 0
20 1 0 0
21 1 0 1
22 1 1 1
23 1 0 1
24 1 0 0
25 1 1 0
26 1 0 1
27 1 0 1
28 1 0 1
29 1 0 0
30 1 0 0
31 1 1 1
32 1 0 1
33 1 0 1
34 1 1 0
35 1 0 0
attr(,"assign")
[1] 0 1 2
attr(,"contrasts")
attr(,"contrasts")$Sample
[1] "contr.treatment"
attr(,"contrasts")$Sex
[1] "contr.treatment"
> colnames(design)
[1] "(Intercept)" "SampleCase" "SexF"
> Lmfit<-lmFit(autosome.Mvalues.noSNPs, design) ## using M values
> fit<-eBayes(Lmfit)
>
top.50<-topTable(fit,coef=2,adjust.method="fdr",number=50,sort.by="B")
> top.50
-- output of sessionInfo():
> sessionInfo()
R version 3.1.0 (2014-04-10)
Platform: x86_64-w64-mingw32/x64 (64-bit)
locale:
[1] LC_COLLATE=English_United States.1252 LC_CTYPE=English_United
States.1252 LC_MONETARY=English_United States.1252
[4] LC_NUMERIC=C LC_TIME=English_United
States.1252
attached base packages:
[1] parallel stats graphics grDevices utils datasets
methods base
other attached packages:
[1] FlowSorted.Blood.450k_1.2.0 quadprog_1.5-5
[3] DMRcate_1.0.1
DMRcatedata_1.0.0
[5] limma_3.20.8 ks_1.9.2
[7] rgl_0.93.1098 mvtnorm_1.0-0
[9] misc3d_0.8-4
KernSmooth_2.23-12
[11] minfiData_0.6.0
IlluminaHumanMethylation450kanno.ilmn12.hg19_0.2.1
[13] IlluminaHumanMethylation450kmanifest_0.4.0 minfi_1.10.2
[15] bumphunter_1.4.2 locfit_1.5-9.1
[17] iterators_1.0.7 foreach_1.4.2
[19] Biostrings_2.32.1 XVector_0.4.0
[21] GenomicRanges_1.16.4
GenomeInfoDb_1.0.2
[23] IRanges_1.22.10
lattice_0.20-29
[25] Biobase_2.24.0
BiocGenerics_0.10.0
loaded via a namespace (and not attached):
[1] annotate_1.42.1 AnnotationDbi_1.26.0 base64_1.1
beanplot_1.1 codetools_0.2-8
[6] DBI_0.2-7 digest_0.6.4 doRNG_1.6
genefilter_1.46.1 grid_3.1.0
[11] illuminaio_0.6.0 MASS_7.3-33 matrixStats_0.10.0
mclust_4.3 multtest_2.20.0
[16] nlme_3.1-117 nor1mix_1.1-4 pkgmaker_0.22
plyr_1.8.1 preprocessCore_1.26.1
[21] R.methodsS3_1.6.1 RColorBrewer_1.0-5 Rcpp_0.11.2
registry_0.2 reshape_0.8.5
[26] rngtools_1.2.4 RSQLite_0.11.4 siggenes_1.38.0
splines_3.1.0 stats4_3.1.0
[31] stringr_0.6.2 survival_2.37-7 tools_3.1.0
XML_3.98-1.1 xtable_1.7-3
[36] zlibbioc_1.10.0
--
Sent via the guest posting facility at bioconductor.org.
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Thank you, Dr. Smyth.