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bigbio / pIR

Estimation of isoelectric point of peptides and proteins using Support vector machines
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Computation warning #13

Closed ypriverol closed 8 years ago

ypriverol commented 8 years ago

This issue has been reported by email by Chris Caffalette:

Thank you for answering my email despite the weekend. Right now I am just using the basic sequenced-based pI determination, and I am actually only entering the very short sequences or the example sequences so far. I also note for the example sequence AGAAPYVQAFDSLLAGPVAE a different pI than your example. It was a long process to install all of the necessary components to prepare for this package, devtools, kernlab, bioclite, etc. So maybe there was an installation error in one of those processes that leads to an error in the final pIR package. If you also think that installation is the problem, no worries with trying to troubleshoot, I will just have to go through the installation again.

Thanks! Chris

pI <- pISVMpeptide(sequence = "RRR", model="default") Warning message: In Ops.factor(left, right) : ‘*’ not meaningful for factors pI [1] 6.3521

pI <- pISVMpeptide(sequence = "AGAAPYVQAFDSLLAGPVAE", model="default") Warning message: In Ops.factor(left, right) : ‘*’ not meaningful for factors pI [1] 3.354431

ypriverol commented 8 years ago

Another comment:

I do not see an error when using the iterative method, and the values coincide with your example (below). This may be sufficient for my use versus the SVM models.

library(pIR) sequence <- "AADCEVEQWDSDEPIPAK" pIvalues <- computeAllIterativeValues(seq = sequence)

pIvalues method values 1 solomon 3.416 2 rodwell 3.375 3 emboss 3.532 4 lehninger 3.371 5 grimsley 3.301 6 patrickios 3.422 7 DtaSelect 3.785 8 toseland 3.357 9 thurlkill 3.478 10 nozaki_tanford 3.645

sequence <- "AADCEVEQWDSDEPIPAK" pIvalues <- computeAllIterativeValues(seq = sequence)

The result will be...

pIvalues method values 1 solomon 3.4161 2 rodwell 3.3749 3 emboss 3.5322 4 lehninger 3.3711 5 grimsley 3.3012 6 patrickios 3.4220 7 DtaSelect 3.7848 8 toseland 3.3571 9 thurlkill 3.4784

10 nozaki_tanford 3.6445

ypriverol commented 8 years ago

A new suppress to the warning section has been committed.