Hi,

I am having some problems reading quantarray files in Limma. I can read the
files and perform the analysis but after I finish the analysis and try to
visualize the results using the function topTable I don't see the IDs of my
genes. Any help is appreciated.

The code I am using is:

library(marray)
library(limma)
library(convert)

#read target info again (in a format that limma will understand)
targets <- readTargets("target.txt")

#read data
data2 <- read.maimages(targets$FileName, source="quantarray")

#normalize data within arrays
MA <- normalizeWithinArrays(data2, method = "median")

#normalize between arrays
MA.loess <- normalizeWithinArrays(data2, method="loess")

#statistical analysis
design <- modelMatrix(targets, ref="FSEM")
fit <- lmFit(MA.loess, design)
fit2 <- eBayes(fit)
topTable(fit2, n=24)


The results I get are something like this:
      Array.Row Array.Column Row Column Name      logFC   AveExpr
t      P.Value  adj.P.Val        B
2979          1            4   4      3   NA  0.7650399 11.317572 10.440014
5.369919e-07 0.02477036 5.720621
10025         3            3  14     12   NA  1.1112795 11.607394  9.107978
2.053595e-06 0.04430252 4.764422
6803          2            4   3     14   NA  1.4909917 10.853941  8.794212
2.881277e-06 0.04430252 4.511043
6701          2            3  31      5   NA  0.8038261 10.822350  8.447169
4.237030e-06 0.04447141 4.216955
1848          1            2  29     19   NA  0.6509226 10.366205  8.333438
4.820435e-06 0.04447141 4.117292
40791        11            3  14     26   NA -0.4895443 10.247273 -7.356528
1.545782e-05 0.07290949 3.189524
6143          2            3  13      5   NA  0.6494603 10.863728  7.295153
1.669200e-05 0.07290949 3.126713
13769         4            3  11      5   NA  0.9898807 13.038236  7.178328
1.934401e-05 0.07290949 3.005600
3544          1            4  22     10   NA  0.5205167 10.318964  6.871036
2.873648e-05 0.07290949 2.677103

Best regards,

-- 
Michael Waisberg, MD, PhD
Visiting research fellow
Laboratory of Immunogenetics
Twinbrook II, National Institute of Allergy and Infectious Diseases
Rockville, MD 20852


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"I do not fear computers. I fear the lack of them."
Isaac Asimov

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