[BioC] using limma to analyze microarray data

[xiayu [guest]]

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

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