PSEA deconvolution; some of the coefficient is NA?
0
0
Entering edit mode
kavator ▴ 30
@kavator-22955
Last seen 21 months ago
Singapore

Hi folks i tried deconvoluting with PSEA package

first, according to vignette; i defined the markers before this; none of the probesets contain any NA values;

      neuronref<-marker(neuronprobeset,expr=counts,targetMean = 100)
    mgref<-marker(mgprobeset,expr=counts,targetMean = 100)

 astrocyteref<-marker(astrprobeset,expr=counts,targetMean = 100)

Defined the groups (corresponding to my expression matrix as well:

    x<-c(0,1)
groups<-rep(x,each=4)

However when i defined linear model

model.group0 <- lm(counts["Apoe",] ~ neuronref + astrocyteref +
           mgref,subset=which(groups==0))

I realised that mgref is NA and

summary (model.group0)

only shows Estimates of neuronref, astrocyteref. The rest; whether it is p-values or degree of freedom are NA. this problem does not happen if i remove subset=which(groups==0);

Would appreciate some advice, thank you.

PSEA Deconvolution • 792 views
ADD COMMENT
0
Entering edit mode

Hi, most probably what is happening is that your dataset does not contain enough samples. Here you are trying to fit (an intercept plus) 3 population-specific markers (neuronref, astrocyteref and mgref) using 4 samples (which(groups==0)), which is like fitting a straight line across 2 data points, leaving no residual degrees of freedom (hence the problem disappearing when you suppress the "subset" option).

Just 1 more sample would (technically) allow you to fit the model but in practice, performing deconvolution will typically require dozens of samples (the exact number depend on various parameters, like e.g. the level of noise of your expression levels).

ADD REPLY

Login before adding your answer.

Traffic: 796 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6