R version 2.15.0 (2012-03-30) Platform: x86_64-pc-mingw32/x64 (64-bit) locale: [1] LC_COLLATE=Spanish_Spain.1252 LC_CTYPE=Spanish_Spain.1252 [3] LC_MONETARY=Spanish_Spain.1252 LC_NUMERIC=C [5] LC_TIME=Spanish_Spain.1252 attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] limma_3.12.3 lumiHumanIDMapping_1.10.0 [3] arrayQualityMetrics_3.12.0 lumiHumanAll.db_1.18.0 [5] org.Hs.eg.db_2.7.1 RSQLite_0.11.4 [7] DBI_0.2-7 annotate_1.34.1 [9] AnnotationDbi_1.18.4 lumi_2.8.0 [11] nleqslv_2.0 methylumi_2.2.0 [13] ggplot2_0.9.3.1 reshape2_1.2.2 [15] scales_0.2.3 Biobase_2.16.0 [17] BiocGenerics_0.2.0 loaded via a namespace (and not attached): [1] affy_1.34.0 affyio_1.24.0 affyPLM_1.32.0 [4] beadarray_2.6.0 BeadDataPackR_1.8.0 bigmemory_4.2.11 [7] BiocInstaller_1.4.9 Biostrings_2.24.1 bitops_1.0-5 [10] BSgenome_1.24.0 Cairo_1.5-2 cluster_1.14.4 [13] colorspace_1.2-2 dichromat_2.0-0 digest_0.6.3 [16] DNAcopy_1.30.0 genefilter_1.38.0 GenomicRanges_1.8.13 [19] genoset_1.6.0 grid_2.15.0 gtable_0.1.2 [22] hdrcde_2.16 Hmisc_3.10-1.1 hwriter_1.3 [25] IRanges_1.14.4 KernSmooth_2.23-10 labeling_0.2 [28] lattice_0.20-6 latticeExtra_0.6-24 MASS_7.3-23 [31] Matrix_1.0-12 mgcv_1.7-24 munsell_0.4 [34] nlme_3.1-108 plyr_1.8 preprocessCore_1.18.0 [37] proto_0.3-10 RColorBrewer_1.0-5 RCurl_1.95-4.1 [40] Rsamtools_1.8.6 rtracklayer_1.16.3 setRNG_2011.11-2 [43] splines_2.15.0 stats4_2.15.0 stringr_0.6.2 [46] survival_2.37-4 SVGAnnotation_0.93-1 tools_2.15.0 [49] vsn_3.24.0 XML_3.98-1.1 xtable_1.7-1 [52] zlibbioc_1.2.0 -- output of sessionInfo(): Hi, I'm trying to perform an analysis of differential expression between control and patients groups from Illumina microarray data. I have read the vignette of the "lumi" package and some others works related to Illumina microarrays but I'm still not sure if I have to use gene profile or probe profile files. What are the advantages or disadvantages of each one? Which one is the most adequate for this kind of analyses? Thank you very much in advance, Francisco. -- Sent via the guest posting facility at bioconductor.org.