User: aluesley1
aluesley1 • 50
- Reputation:
- 50
- Status:
- New User
- Location:
- Last seen:
- 1 year, 3 months ago
- Joined:
- 1 year, 5 months ago
- Email:
- a********@sheffield.ac.uk
Posts by aluesley1
<prev
• 6 results •
page 1 of 1 •
next >
0
votes
1
answer
1.0k
views
1
answers
... Thank you so much for this. It's a bit frustrating and misleading that it's not a true paired analysis and I appreciate the time you have put into checking this is the case.
I'm going to have an attempt to perform the analysis myself using edgeR as it is part of my MSc research project and I would ...
written 17 months ago by
aluesley1 • 50
0
votes
1
answer
1.0k
views
1
answers
... Hello! Yes it is a continuation from that. I used a workflow for TCGAbiolinks to process the matched data. I have used it before for unmatched normal-tumour samples and it has worked.
Here is what I have used -
Matched.Samples.Normal <- subset(prep.BRCA.normal,
...
written 17 months ago by
aluesley1 • 50
2
votes
1
answer
1.0k
views
1
answer
... I am attempting to do a DEA analysis of matched paired BRCA normal tumour samples using TCGAbiolinks. When I do an analysis of my samples using this formula
dataDEGsMatched <- TCGAanalyze_DEA(mat1 = MatchedTPdataFilt,
mat2 = MatchedNTdataFilt,
...
written 17 months ago by
aluesley1 • 50
• updated
17 months ago by
Kevin Blighe ♦ 52k
1
vote
1
answer
996
views
1
answers
... Ah thank you so much, such a silly error!
When I used GDCDataCommons to identify files for matched paired samples for gene expression it came back with 112 but using the correct code with TCGAbiolinks find 113 which is a bit confusing. ...
written 17 months ago by
aluesley1 • 50
5
votes
1
answer
996
views
5 follow
1
answer
... I am trying to use BRCA data downloaded using TCGAbiolinks to do a differential expression analysis.
I want to do an analysis of the matched-paired tumour-normal samples but can't work out how to identify these cases from the samples I have.
This is the code I have so far and my attempt to subset ...
written 17 months ago by
aluesley1 • 50
• updated
17 months ago by
Kevin Blighe ♦ 52k
7
votes
2
answers
1.4k
views
2
answers
... Hi, sorry if this is a bit basic but I'm very new to R.
I am working in Rstudio and I have gene expression data downloaded using TCGAbiolinks, I have downloaded it and prepared it into a RangedSummarizedObject so it includes the clinical data.
I want to subset the data based on this clinical data ...
written 18 months ago by
aluesley1 • 50
• updated
18 months ago by
Friederike ♦ 5.2k
Latest awards to aluesley1
No awards yet. Soon to come :-)
Use of this site constitutes acceptance of our User
Agreement
and Privacy
Policy.
Powered by Biostar
version 2.3.0
Traffic: 1992 users visited in the last hour