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Error in optimHess(par = init, fn = nbinomFn, gr = nbinomGr, x = x, y = y, : non-finite value supplied by optim #9

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ELMMA-FUNNY opened this issue May 18, 2023 · 0 comments

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@ELMMA-FUNNY
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ELMMA-FUNNY commented May 18, 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

@ELMMA-FUNNY ELMMA-FUNNY changed the title Error in make.names(col.names, unique = TRUE) Error with sample data May 19, 2023
@ELMMA-FUNNY ELMMA-FUNNY changed the title Error with sample data Error with sample data and my data May 19, 2023
@ELMMA-FUNNY 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
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