[BioC] problem with large logFC value

[sgonzalez at ira.cinvestav.mx]

Dear all,

I am doing DGE multifactorial analysis with EdgeR but I have a problem
with somes locus I obtained a large logFC value , perhaps because any
comparision there is some zero.
Is this possible? or maybe I have some error

Thank for your help, waiting your response.
Regards,

This is the scrip that I am using:

d.all<- readDGE(counts.all, skip = 5, comment.char = "!")
colnames(d.all$counts)<-counts.all[,3]
cpmd.all<-cpm(d.all)
d.all <- d.all[rowSums(cpmd.all > 1) >= 2, ]
d.all<- calcNormFactors(d.all)
designall<-model.matrix(~time+time:d.all$samples$group)
d.all <- estimateGLMCommonDisp(d.all, designall)
glmfit.all <- glmFit(d.all, designall,dispersion = d.all$common.dispersion)
lrt.all <- glmLRT(d.all, glmfit.all, coef=4)
topTags(lrt.all,sort.by = "logFC")
	logConc      logFC       LR      P.Value          FDR
AT1G22220 -12.30768 -144269488 62.70746 2.398056e-15 2.995171e-12
AT1G08430 -13.45102 -144269487 37.11160 1.115581e-09 2.960891e-07
AT4G11180 -13.84678  144269487 38.22337 6.309211e-10 1.835116e-07
AT5G41880 -13.36909 -144269486 33.88640 5.842556e-09 1.255052e-06
AT1G04610 -13.41465 -144269486 33.44700 7.323248e-09 1.480900e-06
AT2G24850 -14.18267 -144269486 25.85859 3.673666e-07 3.979742e-05
AT5G44635 -13.98784 -144269486 24.61663 6.994557e-07 6.736796e-05
AT1G35690 -13.60305  144269486 27.92875 1.258656e-07 1.590776e-05
AT1G67328 -13.27975 -144269486 24.43246 7.696091e-07 7.262716e-05
AT1G51460 -13.77582 -144269486 24.12274 9.038647e-07 8.123359e-05

sessionInfo()
R version 2.14.1 (2011-12-22)
Platform: x86_64-pc-linux-gnu (64-bit)

locale:
 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C
 [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8
 [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8
 [7] LC_PAPER=C                 LC_NAME=C
 [9] LC_ADDRESS=C               LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C

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

other attached packages:
[1] edgeR_2.5.5  limma_3.10.3

loaded via a namespace (and not attached):
[1] tools_2.14.1


Sandra Isabel Gonzalez Morales
Graduet Student PhD
Centro de Investigacion y de Estudios Avanzados del I.P.N
Laboratorio Nacional deGenomica
para la Biodiversidad
Km. 9.6 Libramiento Norte Carretera Irapuato-Leon
Irapuato, Gto. México



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