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Hello,when I download the sample data from github and run it with code :
Rscript DTEG.R sample_data/ribo_counts.txt sample_data/rna_counts.txt sample_data/sample_info.txt 1
It works good.
But when I use my data with similary code:
Rscript DTEG.R RTCB_data/ribo_counts.txt RTCB_data/rna_counts.txt RTCB_data/sample_info.txt 1
Error in optimHess(par = init, fn = nbinomFn, gr = nbinomGr, x = x, y = y, :
non-finite value supplied by optim
Calls: lfcShrink ... -> apeglm.single -> optimNbinomHess -> optimHess
In addition: Warning messages:
1: In nbinomGLM(x = x, Y = YNZ, size = size, weights = weightsNZ, offset = offsetNZ, :
the line search routine failed, possibly due to insufficient numeric precision
2: In nbinomGLM(x = x, Y = YNZ, size = size, weights = weightsNZ, offset = offsetNZ, :
the line search routine failed, possibly due to insufficient numeric precision
Execution halted
I don't know why sample data could run with error and how to solve it, could you help me?
The text was updated successfully, but these errors were encountered:
ELMMA-FUNNY
changed the title
Error in make.names(col.names, unique = TRUE)
Error with sample data
May 19, 2023
ELMMA-FUNNY
changed the title
Error with sample data
Error with sample data and my data
May 19, 2023
ELMMA-FUNNY
changed the title
Error with sample data and my data
Error in optimHess(par = init, fn = nbinomFn, gr = nbinomGr, x = x, y = y, : non-finite value supplied by optim
May 19, 2023
Hello,when I download the sample data from github and run it with code :
Rscript DTEG.R sample_data/ribo_counts.txt sample_data/rna_counts.txt sample_data/sample_info.txt 1
It works good.
But when I use my data with similary code:
Rscript DTEG.R RTCB_data/ribo_counts.txt RTCB_data/rna_counts.txt RTCB_data/sample_info.txt 1
Error in optimHess(par = init, fn = nbinomFn, gr = nbinomGr, x = x, y = y, :
non-finite value supplied by optim
Calls: lfcShrink ... -> apeglm.single -> optimNbinomHess -> optimHess
In addition: Warning messages:
1: In nbinomGLM(x = x, Y = YNZ, size = size, weights = weightsNZ, offset = offsetNZ, :
the line search routine failed, possibly due to insufficient numeric precision
2: In nbinomGLM(x = x, Y = YNZ, size = size, weights = weightsNZ, offset = offsetNZ, :
the line search routine failed, possibly due to insufficient numeric precision
Execution halted
I don't know why sample data could run with error and how to solve it, could you help me?
Here are my files.
ribo_counts.txt
rna_counts.txt
sample_info.txt
Thanks,
ELMMY-FUNNY
The text was updated successfully, but these errors were encountered: