User: Robert Baer

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Robert Baer70
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Posts by Robert Baer

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Windows 10 openCyto Install: installation path not writeable, unable to update packages: boot, Matrix, mgcv
... I get the error in the title when I try to install the openCyto package or when I do a straight forward run of biocLite() with no arguments. In the case of openCyto I get the message at the end after an appaently successful install of openCyto.  Subsequently, "library(openCyto) fails ostensibly bec ...
opencyto bioclite package installation written 8 weeks ago by Robert Baer70 • updated 8 weeks ago by ekwame0010
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Error executing flowcore vignette
... I've been working my way through the flow core demo codec and encountered a problem on line 157: > summary(filter(smaller[[1]],rectGate %&% morphGate)) Error in as.vector(data) :    no method for coercing this S4 class to a vector > summary(filter(smaller[[1]],rectGate & morphGate)) F ...
flowcore software error vignette written 8 weeks ago by Robert Baer70 • updated 8 weeks ago by Jiang, Mike1.0k
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GO.db install fails in Windows 10 on second drive
... In installing and updating  bioconductor packages the dependency GO.db fails on widows on what looks like a parsing error brought about by a space in the path on E: drive.  I don't know if this is because the linux equivalent is "/e/program files/..." to the Windows "E:\progem Files\..." But, wheth ...
go software error windows10 written 8 months ago by Robert Baer70
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Comment: C: flowViz and grid
... Thanks as always for the quick feedback and suggestions. Thanks also for mentioning the future of flowViz --> ggcyto transition.  Somehow, I've missed ggcyto up until now.  I'm trying to put so much information together (as someone completely new to flow optometry) that these sorts of tips are e ...
written 16 months ago by Robert Baer70
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flowViz and grid
... When plotting flowFrames, I sometimes get the warning, "Binning grid too coarse for current (small) bandwidth: consider increasing 'gridsize'. I have a general sense of what this is telling me in terms of the density plot, but I cannot figure out how to set the gridsize from the high order plotting ...
flowcore flowviz flow cytometry written 16 months ago by Robert Baer70 • updated 16 months ago by Jiang, Mike1.0k
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parsing flowFrame@description in flowCore
... # flowCore’ version 1.38.1 Steps to reproduce: 1. Read an .fcs file created with a BioRad S3 cell sorter using f <- read.FCS(.) # Names of  in flowFrame names(f@description)   [1] "FCSversion"        "$BEGINANALYSIS"    "$ENDANALYSIS"        [4] "$BEGINDATA"        "$ENDDATA"          "$BEGIN ...
flowcore fcs file @description written 18 months ago by Robert Baer70 • updated 18 months ago by Jiang, Mike1.0k
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Answer: A: read.FCS fails on BioRad FCS files
... Beautiful! I've now installed  flowCore Version: 1.35.12 and the original  BioRad S3 cell sorter file appears to read seamlessly.   Thanks for making your package so accessible.  We are grateful for your contributions.   Biorad tech support reports to me that they too are now able to read files wi ...
written 2.1 years ago by Robert Baer70
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Answer: A: read.FCS fails on BioRad FCS files
... Thanks, again.  I have contacted ProSort support to see what I can get accomplished.  Your patience with my questions greatly appreciated.  I have referenced this discussion for their edification.     ...
written 2.2 years ago by Robert Baer70
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Answer: A: read.FCS fails on BioRad FCS files
... Follow-up The ProSort software does not support float/double saving. I have investigated the headers of these ProSort FCS files, and can provide more detail on what I think is happening. flowCore and read.FCS() are apparently not having difficulty reading data, but rather are having difficulty rea ...
written 2.2 years ago by Robert Baer70
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Comment: C: read.FCS fails on BioRad FCS files
... Thanks.  That is at least a start toward a possible resolution.   I don't know yet what the save options are on the Biorad (ProSort) software, but I'll check it out .  You seem to be telling me that the solution lies on the export side, not the import side.  This implies that the fcs format saves v ...
written 2.2 years ago by Robert Baer70

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