User: biomiha

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biomiha20
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UK/Cambridge
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2 weeks, 5 days ago
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2 years, 8 months ago
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Posts by biomiha

<prev • 28 results • page 1 of 3 • next >
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Comment: C: limma - blocking or regressing out nuisance variable
... Thank you both for your replies. Given that a surprising number of people are starting to use tools like Seurat for bulk RNA sequencing (I think it's the ease of generating the object and running the analysis) this is important to know for those of us with biology backgrounds. Cheers. ...
written 20 days ago by biomiha20
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limma - blocking or regressing out nuisance variable
... Hi, We're analysing some RNA-seq data using limma voom. The design of the study is very similar to https://support.bioconductor.org/p/52920/. In the past I have used blocking (subject and treatment or time point) and then used voom with duplicateCorrelation. This time in addition to subject and tre ...
limma voom rna-seq written 20 days ago by biomiha20 • updated 20 days ago by James W. MacDonald50k
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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 12 weeks ago by biomiha20
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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 3 months ago by biomiha20
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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 3 months ago by biomiha20
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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 3 months ago by biomiha20 • updated 3 months 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 17 months ago by biomiha20
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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 17 months ago by biomiha20
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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 17 months ago by biomiha20
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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 17 months ago by biomiha20

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Popular Question 11 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 23 months ago, created a question with more than 1,000 views. For Which package to run blast

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