User: SamGG

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SamGG90
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France
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1 month ago
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3 years, 8 months ago
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s***************@inserm.fr

Posts by SamGG

<prev • 28 results • page 1 of 3 • next >
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Comment: C: Please help me verify my compensation and spill matrices makes sense ( openCyto
... For sure, it sounds quite strange that the choice of fluorochromes leads to so many cross talk. I think the compensation using the spillover function might be tricky. Double check the fact "you'll need the single stained controls and the unstained control to calculate the spillover matrix with spill ...
written 5 weeks ago by SamGG90
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Answer: A: Please help me verify my compensation and spill matrices makes sense ( openCyto
... Based on the code available at https://github.com/RGLab/flowCore/blob/23d64cbb635ea7bb131b1047d2b97007b9813d93/R/flowFrame-accessors.R#L437, the compensation matrix is applied but does not seem to be assigned to the header of the FCS files. So what you observed makes sense to me. ...
written 5 weeks ago by SamGG90
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Comment: C: How to find Geometric Mean from gated Quantibeads
... This might help you to answer and improve the function. > log(0) [1] -Inf > log(-1) [1] NaN Warning message: In log(-1) : NaNs produced   ...
written 3 months ago by SamGG90
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Comment: C: How to find Geometric Mean from gated Quantibeads
... geometric.means is the name of customised function. fr is the name of its unique argument. As stated by Mike, getStats sends a flowFrame to geometric.means while getStats goes through.the workspace alias gs. Within the code of geometric.means, fr is the name of the variable that contains the flowFra ...
written 3 months ago by SamGG90
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Comment: C: FlowCore/FlowViz: How do I skip plotting of empty populations that would otherwi
... I was wrong, bc is a flowSet. Filtering upon the number of rows (aka events) should do the job. ff.ok <- fsApply(bc, nrow) > 100 # for a better estimation table(ff.ok) # always report when filtering dpl <- densityplot(IndividualID ~ `FITC.A`, bc[ff.ok]) # should be ok   ...
written 4 months ago by SamGG90
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Answer: A: FlowCore/FlowViz: How do I skip plotting of empty populations that would otherwi
... Hi, bc is a flowFrame. When it is empty, nrow(bc) should return zero. ...
written 4 months ago by SamGG90
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Comment: C: Limma is doing the right way to calculate the fold change?
... Interesting related answer. HTH ...
written 4 months ago by SamGG90
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Comment: C: Limma is doing the right way to calculate the fold change?
... @Bioinformatics Although limma sounds easy and convenient, you should encode your design carefully. What I like is to use named values as "Ctrl" and "Treat" instead of 1 and 0, and to define the difference I want to look at using makeContrasts() instead of relying on the default contrast convention. ...
written 5 months ago by SamGG90
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Comment: C: Limma is doing the right way to calculate the fold change?
... @Bioinformatics did you try to swap your design? May be it's what you are looking for ;-) model.matrix(~c(rep(0,2),rep(1,2))) ...
written 5 months ago by SamGG90
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Answer: A: can a function outliers be applied for a flowframe?
... Hi, If you know which function you want to apply, then you can apply to the expression matrix of the flowframe (by use of exprs()) or to a flowset. I guess you should take a look at fsApply(). Best. ...
written 5 months ago by SamGG90

Latest awards to SamGG

Scholar 2.1 years ago, created an answer that has been accepted. For A: samr: understanding scoring line not parallel to diagonal; reproduce example C
Scholar 2.1 years ago, created an answer that has been accepted. For A: Problem with HDF5 and ncdfFlow

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