Entering edit mode
michael waisberg
▴
30
@michael-waisberg-1889
Last seen 10.5 years ago
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
_________________________________________
"I do not fear computers. I fear the lack of them."
Isaac Asimov
[[alternative HTML version deleted]]