User: mark.aaron.fisher

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Posts by mark.aaron.fisher

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Comment: C: getProbeInfo and exprs return matrices and data.frames of different dimensions
... Our team is hoping to apply other types of normalization (e.g., loess, lowess, qspline) in addition to quantile, which is why we're needing to break the oligo::summarize() function out separately from rma. ...
written 3.0 years ago by mark.aaron.fisher0
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Comment: C: getProbeInfo and exprs return matrices and data.frames of different dimensions
... Thanks so much, @james! Do you think it makes sense to apply summarize() to just those probes that A) have probes in the then and B) are PM probes? ...
written 3.0 years ago by mark.aaron.fisher0
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getProbeInfo and exprs return matrices and data.frames of different dimensions
... I'm trying to write a function that can summarize intensity matrices from Affymetrix array types that require the affy package alongside those that require the oligo package to read (incidentally, it's not clear to my why two separate packages are required to accomplish this). The most straightforw ...
affy oligo oligoclasses written 3.1 years ago by mark.aaron.fisher0 • updated 3.1 years ago by James W. MacDonald52k
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Comment: C: sqliteSendQuery error in AnnotationForge bioconductor package
... I believe that worked! Many thanks, James!! ...
written 3.4 years ago by mark.aaron.fisher0
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Comment: C: sqliteSendQuery error in AnnotationForge bioconductor package
... Thanks for the timely reply, James! I was actually in the midst of writing you a personal email when I saw this! I've updated everything now, I believe, and still no dice:   makeDBPackage("HUMANCHIP_DB", affy = TRUE, prefix="primeview",fileName="PrimeView.na34.annot.csv", baseMapType="gbNRef",out ...
written 3.4 years ago by mark.aaron.fisher0
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Comment: C: sqliteSendQuery error in AnnotationForge bioconductor package
... I'm having the same issue with current versions:   makeDBPackage("HUMANCHIP_DB", affy = TRUE, prefix="primeview",fileName="PrimeView.na34.annot.csv", baseMapType="gbNRef",outputDir=".", version = "12.1.0", manufacturer="Affymetrix",manufacturerUrl="http://www.affymetrix.com") baseMapType is gb or ...
written 3.4 years ago by mark.aaron.fisher0

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