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PSEA deconvolution; lmfitst error

Hi all, i've been trying out PSEA deonvolution for expression count matrices; i managed to reach the steps

constructing ref signals

neuref<-marker(neuronprobeset,expr=counts,targetMean = 100)
mgref<-marker(mgprobeset,expr=counts,targetMean = 100)
oligref<-marker(oligprobeset,expr=counts,targetMean = 100)
oligprecref<-marker(oligprecprobeset,expr=counts.wt,targetMean = 100)
astrref<-marker(astrprobeset,expr=counts,targetMean = 100)  
x<-c(0,1)

groups vector matching order of count matrix 

groups<-rep(x,each=4)
model_matrix<- fmm(cbind(neuref,astrref,oligref,mgref,oligprecref),groups)
model_subset<-em_quantvg(c(2,3,4,5), tnv=4, ng=1,int=TRUE)
models<- lmfitst(t(counts), model_matrix, model_subset)

However, i get the error from lmfitst

Error in terms.formula(formula, data = data) : '.' in formula and no 'data' argument

May i know why doesnt the function recognise the count matrices and model_matrix?

rna-seq deconvolution psea linear models
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written by lordoftheflower • lordoftheflower

Just to give a glimpse of what is counts and model_matrix;

> model_matrix
     [,1]      [,2]      [,3]      [,4]      [,5]      [,6]      [,7]      [,8]
[1,]    1  77.87464  81.92817  80.44365  84.78367  81.73639   0.00000   0.00000
[2,]    1 113.03835 113.78130 117.94240 117.07493 115.08640   0.00000   0.00000
[3,]    1  88.31566  93.56363  91.71936  88.96603  92.59896   0.00000   0.00000
[4,]    1  95.29341 100.46533 100.54375  95.17305  98.75164   0.00000   0.00000
[5,]    1 113.15393 113.25545 110.22964 113.06135 115.32752 113.15393 113.25545
[6,]    1 112.82099 109.23296 112.76246 110.13421 105.41650 112.82099 109.23296
[7,]    1 104.87355  97.17250  95.70370  99.29742  98.97727 104.87355  97.17250
[8,]    1  94.62946  90.60065  90.65504  91.50933  92.10532  94.62946  90.60065
          [,9]     [,10]     [,11]
[1,]   0.00000   0.00000   0.00000
[2,]   0.00000   0.00000   0.00000
[3,]   0.00000   0.00000   0.00000
[4,]   0.00000   0.00000   0.00000
[5,] 110.22964 113.06135 115.32752
[6,] 112.76246 110.13421 105.41650
[7,]  95.70370  99.29742  98.97727

[8,] 90.65504 91.50933 92.10532

> head(counts)
     1 2 3 4 5 6 7 8
Gnai3 1446   1332   1013   1286     1386    1050     1228   1210
Cdc45   61     52     50     45       49      54       40     44
Scml2   56     75     53     56       58      44       52     76
Apoh     7     12     10      2        6       7        3     10
Narf  2332   2357   1586   2087     2124    1874     1941   1893
Cav2  1103   1275    716   1086     1004     839      900   1233

i anonymise the colnames which contains samples to 1-8; pls pardon the spacing formatting of colnames

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written by lordoftheflower • lordoftheflower

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