User: zacher@lmb.uni-muenchen.de

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8 years, 7 months ago
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Posts by zacher@lmb.uni-muenchen.de

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Answer: A: Reading GFF using Starr
... Dear Feseha, sorry for the late reply. I am currently on holidays for some weeks. I am going to make the documentation more clear, regarding what is meant by the "feature" argument. I hope, everything works now. Please contact me if you have any further questions on Starr. Best, Benedikt Wolfgan ...
written 8.6 years ago by zacher@lmb.uni-muenchen.de50
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Answer: A: ChIP-chip sequence bias not removed
... Dear Edwin, as I guess from inspecting your code chunck, you did not substract a reference experiment from the IP. To eliminate the sequence-dependent bias you either need to substract a reference experiment (like Mock-IP or genomic input) or apply a sepcific normalization method like MAT, which ...
written 9.2 years ago by zacher@lmb.uni-muenchen.de50
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Answer: A: Error using getMeans function in Ringo/Starr
... Dear Noah, do the annotation and the probeAnno object use the same name for the chromosomes? Regards, Benedikt Noah Dowell schrieb : > Hello All, > > I am having some problems with the getMeans function in the Ringo and Starr > packages not working in my hands with my data set. I ...
written 9.5 years ago by zacher@lmb.uni-muenchen.de50
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Answer: A: Ringo/Starr getProfiles function
... Dear Noah, the writeGFF function does not create a gff annotation, but writes all coloumns of the assayData (intensities in the ExpressionSet) to a gff file. If you do this, you can view the data in one of the established genome Browsers (which take this format). I modified your script (my change ...
written 9.9 years ago by zacher@lmb.uni-muenchen.de50
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Answer: A: Affymetrix Mouse Promoter array / pdInfoBuilder
... Dear Hans-Ulrich, The package affxparser contains functions to read and write bpmap files. The function readBpmap returns a list which also contains the probe sequences. A remapping can e.g. be done with MUMmer or the bioconductor package Biostrings. Here is a short workflow, that you could do wit ...
written 10.0 years ago by zacher@lmb.uni-muenchen.de50

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