[BioC] logFC , Limma (microArray Analysis)

[Gordon K Smyth]

You have to log-transform the data.  The data matrix contains unlogged 
intensities, but limma works with log2-intensities.

The normalization may also be suspect.

Gordon


--------- original message ----------
[BioC] logFC , Limma (microArray Analysis)
BEN HAMDA Cherif cherifbenhamda at gmail.com
Sun Apr 6 18:48:20 CEST 2014

Hello
Hope that everything is good for you !

i have a strange results in my work  ( series_matrix.txt microarray analysis )
and i don't know if it's normal or not !

i get high value (logFC)

               logFC    AveExpr         t      P.Value          adj.P.Val
       B
14990  *184.8393  *279.5879  7.053297 6.558774e-08 0.001457032 -3.553707
11016 *-113.2735*  132.3939 -6.777861 1.404067e-07 0.001559568 -3.588662
583     *565.7128   * 942.2667 -6.602527 2.288115e-07 0.001694349 
-3.611925
21147 -*103.8393*   411.5121 -6.436832 3.639169e-07 0.002021103 -3.634652
2067  -*173.5342*   357.1273 -6.261612 5.958922e-07 0.002647549 -3.659485
5404  -*427.6940  * 464.8182 -6.131110 8.616234e-07 0.002968063 -3.678522

i show my method :

gse <- getGEO(filename='GSE1849-GPL96_series_matrix.txt.gz')

i make the design and after that i make analysis with limma :

library(limma)
fit <- lmFit(exprs(gse), design)
contrast.matrix <- makeContrasts(Normal_ACS = Normal - ACS , 
levels=design)
contrast.matrix
Ctrl_fits <- contrasts.fit(fit, contrast.matrix)
Ctrl_ebFit <- eBayes(Ctrl_fits)
nrow(topTable(Ctrl_ebFit, adjust = "BH", coef = 1, number = Inf)

So it's normal or not ? i made mistake in my R code ? someone can help me?

Thank you so much

Best,
cherif

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