Entering edit mode
Shi, Tao
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720
@shi-tao-199
Last seen 9.6 years ago
Dear Gordon and list,
Please see the example below and R output.? The coefficients for Probe
#2 can't be estimated b/c patient 10 data were missing.? But in fact,
they can be estimated just using data from other 9 patients.? Is there
a way to tell limma to do that?
Thanks!
Tao
library(limma)
dat <- matrix(rnorm(400), ncol=40)
ptID <- factor(rep(1:10, each=4))
day <- factor(rep(1:4,10))
dat[2, 37:40] <- NA
design <- model.matrix(~0+ptID+day)
contrast.matrix <- makeContrasts(day2=day2, day3=day3,day4=day4,
levels=design)
fit1 <- lmFit(dat, design=design)
fit2 <- eBayes(contrasts.fit(fit1, contrast.matrix))
Warning message:
Partial NA coefficients for 1 probe(s)
> fit2$p.value
?????? Contrasts
????????????? day2????? day3????? day4
?? [1,] 0.40027892 0.4917185 0.0387787
?? [2,]???????? NA??????? NA??????? NA
?? [3,] 0.05281279 0.4914354 0.6088744
?? [4,] 0.72648798 0.6816108 0.7551084
?? [5,] 0.35528206 0.7962423 0.9827632
?? [6,] 0.09552328 0.3458950 0.1327465
?? [7,] 0.76918217 0.5945065 0.4511735
?? [8,] 0.40125232 0.1066155 0.1269416
?? [9,] 0.56923379 0.2981261 0.9285374
? [10,] 0.04276991 0.4693320 0.3139434
> fit2$coef
?????? Contrasts
????????????? day2?????? day3???????? day4
?? [1,]? 0.3737307? 0.3054398? 0.921284513
?? [2,]???????? NA???????? NA?????????? NA
?? [3,] -0.8628711 -0.3056396 -0.227256710
?? [4,] -0.1553395? 0.1821986? 0.138509886
?? [5,] -0.4107858? 0.1146613 -0.009593154
?? [6,]? 0.7421089 -0.4188821? 0.668951727
?? [7,] -0.1303084 -0.2364268 -0.334736056
?? [8,] -0.3729581 -0.7182350 -0.679192601
?? [9,]? 0.2528092? 0.4624636? 0.039823091
? [10,] -0.9030535 -0.3214420 -0.447554386
> sessionInfo()
R version 3.0.0 (2013-04-03)
Platform: x86_64-w64-mingw32/x64 (64-bit)
locale:
[1] LC_COLLATE=English_United States.1252? LC_CTYPE=English_United
States.1252??? LC_MONETARY=English_United States.1252
LC_NUMERIC=C?????????????????????????
[5] LC_TIME=English_United States.1252???
attached base packages:
[1] grDevices datasets? splines?? graphics? stats???? tcltk????
utils???? methods?? base????
other attached packages:
[1] limma_3.16.3??? svSocket_0.9-55 TinnR_1.0-5???? R2HTML_2.2.1???
Hmisc_3.10-1.1? survival_2.37-4
loaded via a namespace (and not attached):
[1] cluster_1.14.4? grid_3.0.0????? lattice_0.20-15 svMisc_0.9-69??
tools_3.0.0???