Question: error in DEXSeq fitDispersionFunction()
0
gravatar for Alejandro Reyes
7.0 years ago by
Alejandro Reyes1.7k
Dana-Farber Cancer Institute, Boston, USA
Alejandro Reyes1.7k wrote:
Dear Georg, Thanks for your email and noticing the error. A parameter of the glmnb.fit function (statmod package) changed recently from "start" to "coef.start". That was making some problems in DEXSeq, but I adapted the DEXSeq code to it. Could you try to update to the last version of the svn (1.3.16)? Best wishes, Alejandro ps. I added copy to the Bioconductor mailing list in case someone is interested, could be helpful for people having the same error message > Dear Alejandro, > > some time ago you helped me to solve a problem with > estimateDispersions() in the DEXSeq package. I had to interrupt working > on these data, but now I picked it up again and there seems to be > another problem. This time estimateDispersins does not generate any > results (as fa as I can tell), but without an error message. I attached > my example data, the script and the messages to this mail. It would > extremely nice of you, if you could have a look into it and give me a > hint about what is going on. > > Best wishes, > > Georg >
dexseq • 412 views
ADD COMMENTlink modified 7.0 years ago by Georg Otto120 • written 7.0 years ago by Alejandro Reyes1.7k
Answer: error in DEXSeq fitDispersionFunction()
0
gravatar for Georg Otto
7.0 years ago by
Georg Otto120
Georg Otto120 wrote:
Thanks a lot! Now unfortunately I get a problem at the the size factor estimation step: > bat.counts <- estimateSizeFactors(bat.counts) Error in validObject(cds) : invalid class ?ExonCountSet? object: The featureNames do not match with the geneIDs:exonIDs Are there incompatibilities with the ExonCountSet object and the new version of DEXSeq? Do I have to generate the ExonCountSet again with the new version? Cheers, Georg On 07/08/12 23:06, Alejandro Reyes wrote: > Dear Georg, > > Thanks for your email and noticing the error. A parameter of the > glmnb.fit function (statmod package) changed recently from "start" to > "coef.start". That was making some problems in DEXSeq, but I adapted > the DEXSeq code to it. Could you try to update to the last version of > the svn (1.3.16)? > > Best wishes, > Alejandro > > ps. I added copy to the Bioconductor mailing list in case someone is > interested, could be helpful for people having the same error message > >> Dear Alejandro, >> >> some time ago you helped me to solve a problem with >> estimateDispersions() in the DEXSeq package. I had to interrupt working >> on these data, but now I picked it up again and there seems to be >> another problem. This time estimateDispersins does not generate any >> results (as fa as I can tell), but without an error message. I attached >> my example data, the script and the messages to this mail. It would >> extremely nice of you, if you could have a look into it and give me a >> hint about what is going on. >> >> Best wishes, >> >> Georg >>
ADD COMMENTlink written 7.0 years ago by Georg Otto120
Dear Georg, Sorry for the delay of my answer. But yes, you have to generate the new ExonCountSet with the new version, or alternatively just do: featureNames(ecs) <- paste(geneIDs, exonIDs, sep = ":") rownames(counts(ecs)) <- featureNames(ecs) Best wishes, Alejandro > Thanks a lot! Now unfortunately I get a problem at the the size factor > estimation step: > > > bat.counts <- estimateSizeFactors(bat.counts) > Error in validObject(cds) : > invalid class ?ExonCountSet? object: The featureNames do not match > with the geneIDs:exonIDs > > Are there incompatibilities with the ExonCountSet object and the new > version of DEXSeq? Do I have to generate the ExonCountSet again with > the new version? > > Cheers, > > Georg > > > On 07/08/12 23:06, Alejandro Reyes wrote: >> Dear Georg, >> >> Thanks for your email and noticing the error. A parameter of the >> glmnb.fit function (statmod package) changed recently from "start" to >> "coef.start". That was making some problems in DEXSeq, but I adapted >> the DEXSeq code to it. Could you try to update to the last version of >> the svn (1.3.16)? >> >> Best wishes, >> Alejandro >> >> ps. I added copy to the Bioconductor mailing list in case someone is >> interested, could be helpful for people having the same error message >> >>> Dear Alejandro, >>> >>> some time ago you helped me to solve a problem with >>> estimateDispersions() in the DEXSeq package. I had to interrupt working >>> on these data, but now I picked it up again and there seems to be >>> another problem. This time estimateDispersins does not generate any >>> results (as fa as I can tell), but without an error message. I attached >>> my example data, the script and the messages to this mail. It would >>> extremely nice of you, if you could have a look into it and give me a >>> hint about what is going on. >>> >>> Best wishes, >>> >>> Georg >>> >
ADD REPLYlink written 7.0 years ago by Alejandro Reyes1.7k
Alejandro Reyes scripsit 08/13/2012 01:12 PM: > Dear Georg, > > Sorry for the delay of my answer. > But yes, you have to generate the new ExonCountSet with the new version, > or alternatively just do: This raises the general question of 'can saved serialised (stored to disk) versions of Bioconductor objects be used across different versions of the software'? The general answer is "no", since anything else would be impractical. In particular, package authors may provide facilities for that (e.g. via providing a method for the 'updateObject' function in BiocGenerics). In general, thus, it is good practice to keep the input data in a sufficiently persistent format (e.g. text files) and the code to create the objects. Others might have further views on this... Best wishes Wolfgang Wolfgang Huber EMBL http://www.embl.de/research/units/genome_biology/huber
ADD REPLYlink written 7.0 years ago by Wolfgang Huber13k
On 08/13/2012 05:57 AM, Wolfgang Huber wrote: > Alejandro Reyes scripsit 08/13/2012 01:12 PM: >> Dear Georg, >> >> Sorry for the delay of my answer. >> But yes, you have to generate the new ExonCountSet with the new version, >> or alternatively just do: > > This raises the general question of 'can saved serialised (stored to > disk) versions of Bioconductor objects be used across different versions > of the software'? > > The general answer is "no", since anything else would be impractical. In > particular, package authors may provide facilities for that (e.g. via > providing a method for the 'updateObject' function in BiocGenerics). > > In general, thus, it is good practice to keep the input data in a > sufficiently persistent format (e.g. text files) and the code to create > the objects. > > Others might have further views on this... Perhaps the best strategy depends on purpose and time scale. For active research in rapidly changing fields and over 0-2 years it seems like portable representation of the original data is best, as Wolfgang suggests. For reproducibility of research in the 1-5 year time span, it seems like one would like to archive or retain access to the original software and processing scripts, in addition to the data. Over longer periods it's difficult to find hardware, compilers, etc to make use of old software, and perhaps the best bet is archived, updated objects like the ALL data set that represent a snapshot of partially processed data. This implies that someone with sufficient familiarity with the software has been conscientious enough to provide facilities for updating objects to work with current implementations, or alternatively conservative enough (perhaps because something close enough to the 'right' representation has been identified) not to modify the underlying data representation. Martin > > Best wishes > Wolfgang > > Wolfgang Huber > EMBL > http://www.embl.de/research/units/genome_biology/huber > > _______________________________________________ > Bioconductor mailing list > Bioconductor at r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor -- Computational Biology / Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N. PO Box 19024 Seattle, WA 98109 Location: Arnold Building M1 B861 Phone: (206) 667-2793
ADD REPLYlink written 7.0 years ago by Martin Morgan ♦♦ 23k
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