gesso model in R

Hi I am trying to run a gesso model as discribed here:https://cran.r-project.org/web/packages/gesso/gesso.pdf

This is my code :

tune_model = gesso.cv(G_train, e_train, y_train, grid_size=50, parallel=TRUE, nfolds=3)

My G_train matrix has of size: 17 * 50, y_train and e_train are vectors of length 17 and my model is "binomial"

Sadly I get the following error:

Error in seq.default(log10(lambda_min), log10(lambda_max), length.out
= grid_size) :    'from' must be a finite number

and I don't understand what is the problem would be happy for your help :)

I tried expirementing with different data sets . when my data looked like this:

enter image description here

it worked , but as i wanted to use more variables and incresed my column size for 30 it again produced the error

gesso r

• 1,449 views • link

written 3.1 years ago by Eliza •

There is a step in gesso.cv where it returns Inf, to reproduce the error, try:

seq.default(log10(1), log10(3), length.out = 5)
# [1] 0.0000000 0.1192803 0.2385606 0.3578409 0.4771213

log10(0)
# [1] -Inf
seq.default(log10(0), log10(3), length.out = 5)
# Error in seq.default(log10(0), log10(3), length.out = 5) : 
#   'from' must be a finite number

I am guessing your input data is wrong, provide example data to reproduce the error. Or you can explore their GitHub codes: https://github.com/NataliaZemlianskaia/gesso

• 0 views • link

written 3.1 years ago by zx8754

@zx8754 Hi, my G_train matrix is of size 17*50 it has the values 0 or 1 indicating if a certain SNP is present for a patient ( 17 patients and 50 SNPs). y_train is a vector of length 17 with also values 0 or 1 indicating if a patient is sick or not and the E_train is also a vector of length 17 with values 0 or 1 and it looks simillar to the way thet generated the data . ... so Im a little bit cluless

• 0 views • link

written 3.1 years ago by Eliza •

0 answers

No answers yet.