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ziyili20 / TOAST

Tools for the analysis of heterogeneous tissues
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Applying TOAST on GSE19830 #15

Closed niccolodpdu closed 1 year ago

niccolodpdu commented 1 year ago

Hi Ziyi,

Greeting! I have encountered some problems when trying to replicate the result of applying TOAST on GSE19830 in your paper. A glimpse what I ran in R:

library(GEOquery) library(TOAST)

gsm <- getGEO("GSE19830") data<-exprs(gsm[[1]]) K=3 set.seed(1234) outRF1 <- csDeconv(data, K, TotalIter = 100, bound_negative = TRUE)

But I kept receiving error messages saying 'Error in quadprog::solve.QP(Dmat, t(Xmat[obs, ]) %*% Y[obs, i], Amat, : matrix D in quadratic function is not positive definite!'.

Or, when I use 'data<-2^exprs(gsm[[1]])', I received 'Error in quadprog::solve.QP(Dmat, t(Xmat[obs, ]) %*% Y[obs, i], Amat, : constraints are inconsistent, no solution!'

I'm not sure if I apply TOAST correctly, or if you have done some normalization or standardization beforehand.

Thanks for your consideration!

Best,

Niccolo

niccolodpdu commented 1 year ago

It is sad when people develop something just for publishing a paper & immediately abandon it after the paper got published.

For those who are still puzzled by this problem, please scale the input data to (0,1]