User: liam.salleh

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Posts by liam.salleh

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Comment: C: Merging RNAseq Datasets of Different Depths
... OK thanks for the clarification. Yes I have previously contacted the Seurat authors but they are not currently replying to emails so I will be trying some of the options you suggested while I wait for their reply, thanks for the advice. ...
written 13 months ago by liam.salleh0
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Comment: C: Merging RNAseq Datasets of Different Depths
... Hi Aaron, Thanks for all the replies, So just to clarify, in the case that runCCA does not allow for differential expression between our cells and the reference dataset, our options include: mnnCorrect for reclustering our cells with reference dataset scmap for projection onto the reference data ...
written 13 months ago by liam.salleh0
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Comment: C: Merging RNAseq Datasets of Different Depths
... Hi Aaron, At the moment I am more concerned with the feasibility of using a dataset such as ours, with the different methods. i.e. I would be interested in looking at the output of both mnnCorrect and scmap to see where my cells group, but I am worried about whether the small homogeneous cell popu ...
written 13 months ago by liam.salleh0
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Comment: C: Merging RNAseq Datasets of Different Depths
... Hi Aaron, Thanks for another informative answer. Regarding runCCA , I was under the impression that because it corrects a lower dimensional subspace rather than the expression matrix itself, downstream differential expression analyses were an option. The Satija lab also has a tutorial using runCCA ...
written 13 months ago by liam.salleh0
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Comment: C: Merging RNAseq Datasets of Different Depths
... Hi Davide, Thank you for the response. Yes I previously ran across scmap and do also intend to use it in this case. Would you happen to be aware if my small number of cells would be problematic for using scmap? I have been doing some reading and so far it seems like it should be fine. ...
written 13 months ago by liam.salleh0
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Comment: C: Merging RNAseq Datasets of Different Depths
... Hi Aaron, Thanks for the in depth response. I'll try find out if performing separate runs of salmon would result in batch effects but in the meantime, I just wanted to clarify a couple of things: When you say to use a nearest neighbours approach do you mean, mnnCorrect? or something more simple j ...
written 13 months ago by liam.salleh0
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Merging RNAseq Datasets of Different Depths
... Hi, I have two small single cell datasets containing RNASeq data from 12, and 20 cells respectively, which were manually isolated. Our hope is to potentially project this data onto another, annotated scRNA-seq dataset which should contain these cells, to see where our data falls into the other dat ...
batch effect scran scrnaseq singlecellexperiment sequencing depth written 14 months ago by liam.salleh0 • updated 14 months ago by Aaron Lun24k

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