User: Gabriel Nathan Kaufman, Mr

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Posts by Gabriel Nathan Kaufman, Mr

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Comment: C: Gene symbols on MA-plot
... Hi Dr Smyth, Thanks for your clarification and command strings. However, this order() command sorts based on the p.value. Is there any way to sort on the LogFC values, which end up being the y-coordinates of the MA-plot? In other words, what slot of the data.fit.eb object should I be calling? ...
written 2.4 years ago by Gabriel Nathan Kaufman, Mr60
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Gene symbols on MA-plot
... I would like to include gene symbols on a MA plot in the same manner as is implemented in the volcano plot command. I have been using the plotMA command from the limma package, but the best workaround I have seen involves extracting the point coordinates using the locator function and labelling them ...
limma oligo volcanoplot plot.ma written 2.4 years ago by Gabriel Nathan Kaufman, Mr60 • updated 2.4 years ago by Gordon Smyth32k
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Answer: A: how to get tissue name of cel files?
... I am not sure that you can obtain that information, unless the CEL file was generated in such a manner that it contains a specific annotation. Check the phenoData slot in the ExpressionSet object, because it might be there. A helpful related thread: https://support.bioconductor.org/p/24247/ ...
written 2.5 years ago by Gabriel Nathan Kaufman, Mr60
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Comment: C: read.idat manifest error
... I am pretty sure that the IDAT files are indeed from WG6v2 arrays, since the readIDAT command from the illuminaio package returns "BeadChip 6x2" as the ChipType (console output copied below).             If Dr Ritchie or anyone else can take a closer look at the files themselves, I would be m ...
written 2.5 years ago by Gabriel Nathan Kaufman, Mr60
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read.idat manifest error
... I am trying to read Illumina Human WG6v2 microarray raw IDAT files using the read.idat command implemented in the limma package. However, I encounter an error which seems to come from the BGX manifest file. When I indicate the correct BGX file, I obtain a read.idat error, as seen below in the code e ...
limma illuminaio illumina human wg6v2 written 2.5 years ago by Gabriel Nathan Kaufman, Mr60 • updated 2.5 years ago by Matthew Ritchie690
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iFlow error messages
... When I try to open some FCS files using iFlow, I get several strange error messages, and I am ultimately unable to open the files.... In iFlow, I get a pop-up box that says "Warning: 'signed = FALSE' is only valid for integers of sizes 1 and 2." In the R console, there are some warnings about RGtk2 ...
gui iflow written 5.8 years ago by Gabriel Nathan Kaufman, Mr60
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flowFlowJo error
... When I try to read in a FlowJo (version 7.6.1 for Windows) workspace file into R using the flowFlowJo package, I get a bizarre error that does not seem to be previously described. It appears to be from an underlying R syntax call, but I have not found any reference as to how flowFlowJo generates thi ...
flowflowjo written 5.8 years ago by Gabriel Nathan Kaufman, Mr60
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Answer: A: iFlow/flowCore installation problem
... I can make it work in Terminal somewhat (the iFlow GUI opens up but seems to be buggy -might be because of a Gtk deprecation). However, I can't seem to make it work through the Mac R GUI... What could be causing this? An incompatibility with x64? Here is the console output from the Terminal ro ...
written 6.8 years ago by Gabriel Nathan Kaufman, Mr60
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iFlow/flowCore installation problem
... I recently tried to install the bleeding-edge version of iFlow, and I think I am doing something wrong with one of its dependencies (console copied below). In short, I cannot seem to load flowCore properly, and the problem persists even when I try to re-install it from source. I have gone as far as ...
biobase flowcore iflow written 6.8 years ago by Gabriel Nathan Kaufman, Mr60 • updated 6.8 years ago by Dan Tenenbaum ♦♦ 8.2k
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iFlow and current Bioconductor release
... Dear Chao-Jen, I recently noticed that the iFlow package was back up on the devel branch of Bioconductor, but I got an error message when I tried to install it: > source("http://www.bioconductor.org/biocLite.R") BioC_mirror = http://www.bioconductor.org Change using chooseBioCmirror(). > ...
iflow written 6.8 years ago by Gabriel Nathan Kaufman, Mr60

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Popular Question 2.4 years ago, created a question with more than 1,000 views. For Gene symbols on MA-plot

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