User: liam.salleh
liam.salleh • 0
- Reputation:
- 0
- Status:
- New User
- Last seen:
- 1 year, 2 months ago
- Joined:
- 1 year, 5 months ago
- Email:
- l**********@auckland.ac.nz
Profile information, website and location are not shown for new users.
This helps us discourage the inappropriate use of our site.
Posts by liam.salleh
<prev
• 7 results •
page 1 of 1 •
next >
0
votes
1
answer
894
views
1
answers
... 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 17 months ago by
liam.salleh • 0
0
votes
1
answer
894
views
1
answers
... 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 17 months ago by
liam.salleh • 0
0
votes
1
answer
894
views
1
answers
... 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 17 months ago by
liam.salleh • 0
0
votes
1
answer
894
views
1
answers
... 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 17 months ago by
liam.salleh • 0
0
votes
1
answer
894
views
1
answers
... 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 17 months ago by
liam.salleh • 0
0
votes
1
answer
894
views
1
answers
... 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 17 months ago by
liam.salleh • 0
6
votes
1
answer
894
views
1
answer
... 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 ...
written 17 months ago by
liam.salleh • 0
• updated
17 months ago by
Aaron Lun • 25k
Latest awards to liam.salleh
No awards yet. Soon to come :-)
Use of this site constitutes acceptance of our User
Agreement
and Privacy
Policy.
Powered by Biostar
version 16.09
Traffic: 331 users visited in the last hour