Thank you in advance for answering my question about limma package! The function read.ilmn() reads in probe_file.txt and control_probe_file.txt seperately for illumina microarray data. What if my illumina Gene Expression BeadChip data look like below? How can I use read.ilmn and follow the steps described in limma user guide 15.3? It is just one file containing the columns: TargetID ProbeID sample1_1 sample1_2 sample2_1 sample2_2 control1_1 control1_2 control2_1 control2_2 The partial real data look like below: Illumina Inc. GenomeStudio version 1.9.0 Normalization = none Array Content = HumanHT-12_V4_0_R1_15002873_B.bgx.xml ??????. TargetID ProbeID MIN_Signal-A253-1 AVG_Signal-A253-1 MAX_Signal-A253-1 NARRAYS-A253-1 ARRAY_STDEV-A253-1 BEAD_STDEV-A253-1 Avg_NBEADS-A253-1 Detection-A253-1 MIN_Signal-A253-2 AVG_Signal-A253-2 MAX_Signal-A253-2 NARRAYS-A253-2 ARRAY_STDEV-A253-2 BEAD_STDEV-A253-2 .....then control 1, 2, ... 7A5 6450255 86.3 86.3 86.3 1 NaN 7.886 19 0.87662 79.2 79.2 79.2 1 NaN 9.671 A1BG 2570615 95.2 95.2 95.2 1 NaN 10.632 20 0.9974 90.8 90.8 90.8 1 NaN 12.482 A1BG 6370619 80 80 80 1 NaN 8.377 18 0.14805 83 83 83 1 NaN 10.002 A1CF 2600039 81.7 81.7 81.7 1 NaN 10.706 22 0.37013 82.4 82.4 82.4 1 NaN 12.386 -- output of sessionInfo(): > sessionInfo() R version 3.0.1 (2013-05-16) Platform: i386-w64-mingw32/i386 (32-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] stats graphics grDevices utils datasets methods base other attached packages: [1] limma_3.16.5 -- Sent via the guest posting facility at bioconductor.org.