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7 results for “from:Francesco Ferrari”

[Bioc-devel] RFC: xy2i and i2xy in *cdf packages
Francesco Ferrari · Mar 26, 2007 · bioc-devel

Sorry, I didn't report many details since, as I wrote, the work is still in progress. However our functions will not be included into a novel package. Our functions retrieve information concerning x/y coordinates of PM and MM...

[Bioc-devel] problem with matchprobes:getProbeDataAffy() -
Francesco Ferrari · Aug 25, 2008 · bioc-devel

A few days ago I received a couple of bug reports concerning an error message occurring when using gcrma preprocessing procedure with custom probeset definitions (gahgu133acdf and gahgu133aprobe package). The source of the problem is one single missing probe sequence...

[Bioc-devel] RFC: xy2i and i2xy in *cdf packages
Francesco Ferrari · Apr 12, 2007 · bioc-devel

I found an interesting "trick" adopted within the package mtachprobes to solve this problem... i.e. obtaining chip dimensions information from current versions of CDF packages. Within the package "matchprobes" there's a function named ".lgExtraParanoia" If you read this...

[Bioc-devel] RFC: xy2i and i2xy in *cdf packages
Francesco Ferrari · Mar 26, 2007 · bioc-devel

If xy2i() and i2xy() functions from CDF packages will be deprecated, we could use the indices2xy() and xy2indices() functions from affy package, but they require either "nr" parameter or an affybatch object.... The "nr" parameter, i.e. the size of...

[Bioc-devel] Fwd: PREDA problems reported in the Multiple platform build/check report for BioC 3.7
Francesco Ferrari · Aug 6, 2018 · bioc-devel

Looks like a CRAN package is no more available, and this is triggering a problem with a ?suggested? dependency * checking package dependencies ... ERROR Package suggested but not available: ?samr? which indeed has been removed from CRAN on July 20: https...

[Bioc-devel] EXTERNAL: Fwd: PREDA problems reported in the Multiple platform build/check report for BioC 3.7
Francesco Ferrari · Sep 17, 2018 · bioc-devel

Dear Lori, I already foxed the issue in the devel branch which now gives a clean check: https://bioconductor.org/checkResults/3.8/bioc-LATEST/ The problema was due to a CRAN dependency no more available since July 20, 2018...

[Bioc-devel] What is Bioconductor's position on allowing users to create files in the working directory without an explicit path definition in the filename
Francesco Ferrari · Mar 22, 2019 · bioc-devel

Dear all, if I understand correctly, the main problem stems from the fact that the function has set a default value for "Output.Filename? argument. Would it then be ok to have NO default value for Output.Filename? So as...

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