[BioC] using limma to analyze microarray data
xiayu [guest]
guest at bioconductor.org
Mon Jun 17 16:39:44 CEST 2013
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 â¦â¦.
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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