Hi

I am using limma to analyze Illumina expression data (two groups), and this time I got some really high logFC values for some genes and "low" for others. Example:

Probe       log2 Ratio(logFC)     Moderated t-statistic (t)  Raw p-value    Adjusted p-value     B
ILMN_27575	5443.972	         27.305	               1.81E-06	     0.009621899	-2.29002

ILMN_14823        42.5	                 19.077	               1.00E-05	     0.022251754	-2.32116

The first gene has intensities in one group (3 samples) around 10 000 and in the other group (3 samples) around 5000, and the second gene has intensities around 110 in the first group and around 80 in the second group. 

I have never seen so high logFC values before, are they realistic? Does this values mean that there are big differences combined with hight intensities?

Regards,
Ingrid

R version 2.5.1 (2007-06-27) 
i386-pc-mingw32 

locale:
LC_COLLATE=English_United Kingdom.1252;LC_CTYPE=English_United Kingdom.1252;LC_MONETARY=English_United Kingdom.1252;LC_NUMERIC=C;LC_TIME=English_United Kingdom.1252

attached base packages:
[1] "splines"   "tools"     "stats"     "graphics"  "grDevices" "utils"     "datasets"  "methods"   "base"     

other attached packages:
illuminaHumanv2         GOstats        Category          Matrix         lattice      genefilter        survival 
        "1.2.0"         "2.2.6"         "2.2.3"    "0.999375-2"        "0.16-3"        "1.14.1"          "2.32" 
           RBGL           graph         annaffy            KEGG              GO          xtable    RColorBrewer 
       "1.12.0"        "1.14.2"         "1.8.1"        "1.16.1"        "1.16.0"         "1.5-1"         "1.0-1" 
          limma            lumi        annotate            mgcv            affy          affyio         Biobase 
       "2.10.5"         "1.2.0"        "1.14.1"        "1.3-26"        "1.14.2"         "1.4.1"        "1.14.1" 

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