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rr1859 / R.4Cker

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Error from 4Cker tranAnalysis #37

Open amarsh33 opened 7 years ago

amarsh33 commented 7 years ago

Hello,

I ran 2 different transAnalyses recently for 2 different viewpoints. The one viewpoint worked okay but did give me the following errors (along with the normal output):

Usp5_trans_results=transAnalysis(Usp5_obj,k=20) [1] "Building adaptive windows..." [1] "Normalizing counts..." [1] "Generating synthetic samples...." [1] "Parameter estimation....."

Iter: 1 fn: 3701131.7085 Pars: 0.33333 0.33333 0.33333 0.50000 0.25000 0.25000 0.25000 0.50000 0.25000 0.25000 0.25000 0.50000 1.35778 0.11122 2.17244 0.01167 2.71555 0.02963 solnp--> Solution not reliable....Problem Inverting Hessian. [1] "Warning: only 1 iteration. Using starting parameters" [1] "BED file of highest interacting domains for trans chromosomes are saved in /Volumes/hd2/4C_seq/analysis/4Cker/Usp5_results/" Warning message: In p0 * vscale[(neq + 2):(nc + np + 1)] : longer object length is not a multiple of shorter object length

However, my analysis from the other viewpoint did not complete and gave me some additional errors:

Pxmp2_trans_results=transAnalysis(Pxmp2_obj,k=20) [1] "Building adaptive windows..." [1] "Normalizing counts..." [1] "Generating synthetic samples...." [1] "Parameter estimation....."

Iter: 1 fn: 6322212.6504 Pars: 0.333333 0.333333 0.333333 0.500000 0.250000 0.250000 0.250000 0.500000 0.250000 0.250000 0.250000 0.500000 1.211190 0.063576 1.937904 0.007503 2.422380 0.038934 solnp--> Solution not reliable....Problem Inverting Hessian. [1] "Warning: only 1 iteration. Using starting parameters" Error in state[et[case]] <- which.max(delta[et[case], ]) : replacement has length zero In addition: Warning message: In p0 * vscale[(neq + 2):(nc + np + 1)] : longer object length is not a multiple of shorter object length

I was just wondering what was causing this error that is causing the job to stop running, and what I should be doing to have more iterations through the data so I don't get the warning messages any more either.

rr1859 commented 7 years ago

Hi,

What primary enzyme are you using for the 4C-Seq experiment? In our experience when you use 4bp cutters, you need very high sequencing depth to call trans interactions

amarsh33 commented 7 years ago

Hello,

I used HindIII as my primary enzyme. The depth of sequencing for my replicates did differ though, which may have caused the error.

Thanks. On Aug 20, 2017, at 10:10 PM, Ramya Raviram notifications@github.com<mailto:notifications@github.com> wrote:

Hi,

What primary enzyme are you using for the 4C-Seq experiment? In our experience when you use 4bp cutters, you need very high sequencing depth to call trans interactions

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