User: clevy

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clevy10
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New User
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United States
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1 year, 2 months ago
Joined:
3 years, 9 months ago
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Posts by clevy

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Comment: C: Comparing DE probes from same-platform microarrays
... Thanks, the scatterplot is a good idea. Looks like a good number of overlaps in at least a couple of the contrasts (hundreds of probes) but I'll check out roast() and barcodeplot() too. ...
written 3.4 years ago by clevy10
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Comment: C: Comparing DE probes from same-platform microarrays
... Thanks for your help Aaron! ...
written 3.4 years ago by clevy10
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Comparing DE probes from same-platform microarrays
... I have microarray data from two experiments that differ in the type of tissue that the RNA was extracted from.  In both experiments, tissue was infected with a virus or mock-infected (paired within donors) and we looked for probes that were DE between virus and mock. I am interested in which DE prob ...
microarray limma meta-analysis written 3.4 years ago by clevy10 • updated 3.4 years ago by Gordon Smyth37k
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Question about lumiT warning message
... I am attempting to transform a lumiBatch and got the following warning message: Warning message: In lumiT(B.complete.RAW.lumi) :   Too few probes are detectable based on detection p-values!                           Iteration method will be used for VST. I realize that this is a warning and not an ...
lumi written 3.4 years ago by clevy10
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Comment: C: How does limma deal with missing samples?
... Great, I'm glad things are not always as complicated as they seem. I'll have another go at it.  TissueID is the same thing as donor by the way. Thanks for your help! ...
written 3.5 years ago by clevy10
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Comment: C: How does limma deal with missing samples?
... Great, I'm glad things are not always as complicated as they seem. I'll have another go at it.  TissueID is the same thing as donor by the way. Thanks for your help! ...
written 3.5 years ago by clevy10
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Comment: C: How does limma deal with missing samples?
... Fantastic, I have been following the "Multilevel Experiments" section (pg 51) and it more or less makes sense but I am not sure about the  duplicateCorrelation part.  The difference between my experiment and the example is that each of my subjects is exposed to all conditions, while in the example, ...
written 3.5 years ago by clevy10
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Answer: A: How does limma deal with missing samples?
... Great, that is kind of what I hoped would happen. By "better to analyze all the data at once", do you mean statistically, or more from an interpretation of results perspective? I am keen on the "analyze all at once" approach so I will take a closer look at the Time Course Experiments section on pg4 ...
written 3.5 years ago by clevy10
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Dealing with missing samples in limma and design matrix questions
... Hi Bioconductors, I am working on analyzing data from an Illumina beadchip microarray with samples from the following experimental set-up: 7 tissue donors x 3 treatments x 3 RNA collection time points Treatments: Mock infection, virus A infection, virus B infection RNA collected from tissue at t ...
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Errors when reading CyToF flowSet into flowCore
... BACKGROUND I have four .fcs files from CyToF samples that I have exported from FlowJo 10.0.8. I am using flowCore to read in the samples so that I can then use the Rtsne package to do a t-SNE analysis of the data. I anticipate having a large number of samples to analyze in the future so I would lik ...
flowcore cytof rtsne written 3.8 years ago by clevy10 • updated 3.8 years ago by Jiang, Mike1.2k

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