Hi all,

I'm currently trying to use the package NanoStringDiff to analyse Nanostring nCounter gene expression data.

I have a dataset based on samples from 6 patients (C7, C8, C9, C10, C11, C12), each patient with a treated sample and with a control sample :

     treated id
1    drug    C7
2    CTRL    C7
3    drug    C8
4    CTRL    C8
5    drug    C9
6    CTRL    C9
7    drug    C10
8    CTRL    C10
9    drug    C11
10   CTRL    C11
11   drug    C12
12   CTRL    C12

I would like to detect the effect of the treatment, while correcting for variations between patients.

Based on answers given on other GLM based packages, I've came up with the following design matrix and contrasts, but I'm questionning the validity of this approach.

design.full=model.matrix(~pheno$id + pheno$treated)
design.full

             (Intercept)    pheno$idC11    pheno$idC12   pheno$idC7    pheno$idC8
1            1              0              0             1             0
2            1              0              0             1             0
3            1              0              0             0             1
4            1              0              0             0             1
5            1              0              0             0             0
6            1              0              0             0             0
7            1              0              0             0             0
8            1              0              0             0             0
9            1              1              0             0             0
10           1              1              0             0             0
11           1              0              1             0             0
12           1              0              1             0             0
               pheno$idC9       pheno$treatedCTRL
1              0                0
2              0                1
3              0                0
4              0                1
5              1                0
6              1                1
7              0                0
8              0                1
9              0                0
10             0                1
11             0                0
12             0                1


result=glm.LRT(NanoStringData,design.full,contrast=c(0,0,0,0,0,0,1))

This question have already been adressed here : https://support.bioconductor.org/p/98249/, but I think it stayed unanswered due to few people Using NanoStringDiff.

Thanks for any of your any input, even if you're not familiar with NanoStringDiff.

Yes, that's fine. What exactly is your concern?