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@love-5173
Last seen 7.1 years ago

hi,
I could have things totally mixed up here. I was thinking that GLM
offsets would be positively correlated with log counts.
for instance in edgeR, mglmLS.R:
mu <- exp(beta %*% t(X) + offset)
but it seems offsets from packages EDASeq and cqn are negative
correlated with log counts.
for example some poisson data:
> n <- 1000
> covariate <- rnorm(n,6,.5)
> counts <- replicate(2,rpois(n,exp(covariate)))
> library(EDASeq)
> edaseq.offset <-
withinLaneNormalization(x=counts,y=covariate,which="full",offset=TRUE)
> cor(edaseq.offset[,1],log(counts[,1]+1))
[1] -0.9765923
> library(cqn)
> cqn.offset <-
cqn(counts,x=covariate,lengths=rep(1,n),lengthMethod="fixed",sizeFacto
rs=c(1,1))$offset
> cor(cqn.offset[,1],log(counts[,1]+1))
[1] -0.9950717
So EDASeq and cqn are giving similar results here:
> cor(edaseq.offset[,1],cqn.offset[,1])
[1] 0.9847672
If I give these to the standard glm function as offsets I would expect
the coefficient for 'covariate' to go from 1 to 0. But it gives me
something like a coefficient of 2, and to get zero I have to give it
-1
* offset:
without offset:
> coef(glm(counts[,1] ~ covariate, family="poisson"))
(Intercept) covariate
-0.02735053 1.00467285
with offset:
> coef(glm(counts[,1] ~ covariate, offset=edaseq.offset[,1],
family="poisson"))
(Intercept) covariate
-5.860094 1.954997
> coef(glm(counts[,1] ~ covariate, offset=cqn.offset[,1],
family="poisson"))
(Intercept) covariate
-8.752786 2.457637
with -1 * offset:
> coef(glm(counts[,1] ~ covariate, offset=-edaseq.offset[,1],
family="poisson"))
(Intercept) covariate
5.8253511 0.0498681
> coef(glm(counts[,1] ~ covariate, offset=-cqn.offset[,1],
family="poisson"))
(Intercept) covariate
8.6975896 -0.4482184
thanks for any guidance,
Mike