User: biomiha

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biomiha10
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UK/Cambridge
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1 day, 16 hours ago
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2 years, 6 months ago
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Posts by biomiha

<prev • 26 results • page 1 of 3 • next >
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Comment: C: How to select left hand side of mindensity2 gate
... Hi Mike, One thing I've noticed is that even with the pop argument set to "-" in the `add_pop` API, the gate dimensions themselves are actually set to: Rectangular gate 'nonDebris2' with dimensions: FSC-A: (244703.838155759,Inf) i.e. right hand side. I'm not sure what goes on behind the ...
written 26 days ago by biomiha10
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Comment: C: How to select left hand side of mindensity2 gate
... Thanks Mike. With regards to the fsApply iteration I followed this vignette, which seems to be quite recent https://www.bioconductor.org/packages/devel/bioc/vignettes/flowCore/inst/doc/HowTo-flowCore.pdf. The add_pop API looks like a very good alternative though. ...
written 6 weeks ago by biomiha10
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Comment: C: How to select left hand side of mindensity2 gate
... I've figured out the reason. At least in my version of `openCyto::gate_mindensity2` the last 3 lines of code are: coords <- list(c(g$final_cut, Inf)) names(coords) <- channel return(rectangleGate(coords, filterId = filterId)) Meaning that any positive argument passed to `gate_min ...
written 6 weeks ago by biomiha10
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How to select left hand side of mindensity2 gate
... Hi, I'm trying to use the `gate_mindensity2` from the openCyto package to gate out debris from my .fcs files. I'm using https://flowrepository.org/id/FR-FCM-ZZ36 as an example. I can gate out the debris at the lower end (i.e. left hand side of the gate) but if I want to apply a gate to remove the ...
opencyto mindensity written 6 weeks ago by biomiha10 • updated 6 weeks ago by Jiang, Mike1.2k
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Comment: C: Error in dimnames(x) <- dn : length of 'dimnames' [1] not equal to array exte
... The FCS repository is a good source. I've been using this one (https://flowrepository.org/id/FR-FCM-ZZ36) to play with. ...
written 15 months ago by biomiha10
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Comment: C: Error in dimnames(x) <- dn : length of 'dimnames' [1] not equal to array exte
... Thanks Mike. That works now. Apologies. M ...
written 15 months ago by biomiha10
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Comment: C: Error in dimnames(x) <- dn : length of 'dimnames' [1] not equal to array exte
... So, the reasoning is the same every time you run a FACS compensation panel. You take your controls (cells or beads) that will bind an antibody and you stain them with single colours to generate you single stained samples. Then you run them on the machine and look at all of the detectors to see how m ...
written 15 months ago by biomiha10
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Comment: C: Error in dimnames(x) <- dn : length of 'dimnames' [1] not equal to array exte
... Hi,   I think you get the `Error: Baseline not in this set.` because the unstained control is not specified correctly. If you change that to the index of the unstained control, you'll get the dimnames error again. There is a bug in the spillover function that I'm not able to locate. I know there ...
written 15 months ago by biomiha10
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Comment: C: Error in dimnames(x) <- dn : length of 'dimnames' [1] not equal to array exte
... Thanks SamGG, The thing is that I get the same error with other flowSets, irrespective of how I read them in. So far, I've got the same error with each and every set of FCS files I've tried. The one I used for my reprex was just the code from the flowCore vignette. Do you not get the error with you ...
written 15 months ago by biomiha10
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Error in dimnames(x) <- dn : length of 'dimnames' [1] not equal to array extent
... Hi, I'm trying to use the spillover function from the flowCore package.  I'm not sure what's wrong but any set of compensation samples (i.e. unstained and single stained) I use it on, I always get the same error: Error in dimnames(x) <- dn :       length of 'dimnames' [1] not equal to array e ...
flowcore spillover written 15 months ago by biomiha10 • updated 15 months ago by Jiang, Mike1.2k

Latest awards to biomiha

Popular Question 9 months ago, created a question with more than 1,000 views. For Error in dimnames(x) <- dn : length of 'dimnames' [1] not equal to array extent
Popular Question 21 months ago, created a question with more than 1,000 views. For Which package to run blast

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