User: Djork Clevert

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Djork Clevert210
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Posts by Djork Clevert

<prev • 19 results • page 1 of 2 • next >
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Answer: A: CNV detection using cn.farms for non-affymetrix arrays (custom oligonucleotide a
... Hi Joan, it?s very nice to read that you use our cn.MOPS-algortihm for detecting CNVs in NGS-data. However, just to make sure that we are in the same ballpark: cn.MOPS (Copy Number estimation by a Mixture Of PoissonS) and cn.FARMS (Copy Number Factor Analysis for Robust Microarray Summarization) a ...
written 3.6 years ago by Djork Clevert210
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Conference Announcement - CAMDA 2014
... Dear Colleagues, With great pleasure we announce the 13th International Conference on the Critical Assessment of Massive Data Analysis (CAMDA) in Boston, MA, U.S.A., July 11-12, 2014, held as official Satellite Meeting to 22nd Conference on Intelligent Systems for Molecular Biology (ISMB). CAMDA f ...
genetics cancer written 3.7 years ago by Djork Clevert210
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Farms/Call.INI using oligo package?
... Hi Fraser, the bump at 0.5 stems from probe sets with only one probe. For those is modeling not required ;-) I would recommend not to use them, as they their expression values are probably not reliable. This way you get rip off them: Cheers, Okko SNR <- apply(eset at assayData$se.exprs,1,min) ...
probe affy oligo sim farms written 4.0 years ago by Djork Clevert210
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Answer: A: Farms/Call.INI using oligo package?
... Hi Fraser, I just realized that my previous email was everything else than ?self- explanatory? and on top of that - the workaround contained a typo? Cheers, Okko Please find below the revised code including an example at the end: library(oligo) library(farms) farms <- function(object, backg ...
written 4.0 years ago by Djork Clevert210
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Answer: A: Farms/Call.INI using oligo package?
... Hi Fraser, thanks for reporting this issue. We are aware of this issue. Reason is that since R versions R-3.x.x AffyBatch does no longer support particular array types. We are modifying the FARMS package that array types that no longer supported by AffyBatch objects can be used via the oligo packag ...
written 4.0 years ago by Djork Clevert210
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Answer: A: Can we use DNAcopy to analyse Copy Number Viaration using next generation sequen
... Dear Min, take a look at the vignette of the cn.mops package, there you will find a good manual which also describe the usage of DNAcopy. --okko -- Djork-Arné Clevert, PhD Institute of Bioinformatics Johannes Kepler University Linz Phone: +49 30 4432 4702 Fax: +49 30 6883 5307 Enail: okko@clevert ...
written 4.8 years ago by Djork Clevert210
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Comment: C: Best package or code to filter Affymetrix probes by present calls??
... Hi Miriam, the following code will extract the informative probe sets from the GCRMA ExpressionSet: esetfarms <- qFarms(rawData) INIs <- INIcalls(esetfarms) I.Probes <- getI_ProbeSets(INIS) esetgcrma <- gcrma(rawData) I.esetgcrma <- esetgcrma[I.Probes] Cheers, Okko Am 19.06.2 ...
written 5.4 years ago by Djork Clevert210
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Comment: C: Best package or code to filter Affymetrix probes by present calls??
... Hi Miriam, I suggest you to filter the probe-sets according to their internal consistency -> only rely on probe-sets, where each probe of the set tells you the same story. For further details please read our informative/ non-informative call (I/NI call) paper in Bioinformatics (http://bioinforma ...
written 5.4 years ago by Djork Clevert210
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Comment: C: eset -Affy Mouse Gene 1.0 ST. Array-
... Hi Alex, try to use the alternative CDFs from Brainarray. They provide a better probe mapping which is based on the latest genome and transcriptome information. Install the aCDFs of interest, change rawData at cdfName to the corresponding aCDF, afterwards run the summarization and that's all. Chee ...
written 5.5 years ago by Djork Clevert210
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Comment: C: outlier probes detection
... Hi Andrea, I'm happy to help you in this issue, just let me know if you need any further details regarding the farms algorithm or its assessment. If I recall correct are the probes of a probe-set spatial distributed over the whole HGU133plus2 array surface, so I don't expect that small scratches or ...
written 5.5 years ago by Djork Clevert210

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