## User: biomiha

biomiha20
Reputation:
20
Status:
New User
Location:
UK/Cambridge
Last seen:
4 days, 9 hours ago
Joined:
2 years, 11 months ago
Email:
b******@gmail.com

#### Posts by biomiha

<prev • 29 results • page 1 of 3 • next >
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... This is what I meant:https://bioinformatics.stackexchange.com/questions/5168/seurat-for-clustering-bulk-rna-seq/5204#5204 I truly hope you can stomach the thread and it's not too detrimental to your health. On a serious note, there's no need to be mean. The Seurat authors themselves were suggesting ...
written 7 weeks ago by biomiha20
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... 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 11 weeks ago by biomiha20
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... 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 ...
written 11 weeks ago by biomiha20 • updated 11 weeks ago by James W. MacDonald50k
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... 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 4 months ago by biomiha20
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... 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 5 months ago by biomiha20
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... 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 5 months ago by biomiha20
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... 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 ...
written 5 months ago by biomiha20 • updated 5 months ago by Jiang, Mike1.2k
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... The FCS repository is a good source. I've been using this one (https://flowrepository.org/id/FR-FCM-ZZ36) to play with. ...
written 19 months ago by biomiha20
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... Thanks Mike. That works now. Apologies. M ...
written 19 months ago by biomiha20
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... 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 19 months ago by biomiha20

#### Latest awards to biomiha

Popular Question 13 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 2.1 years ago, created a question with more than 1,000 views. For Which package to run blast

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