User: reubenmcgregor88
reubenmcgregor88 • 0
- Reputation:
- 0
- Status:
- New User
- Last seen:
- 5 months, 1 week ago
- Joined:
- 2 years ago
- Email:
- r***************@gmail.com
Profile information, website and location are not shown for new users.
This helps us discourage the inappropriate use of our site.
Posts by reubenmcgregor88
<prev
• 51 results •
page 1 of 6 •
next >
2
votes
1
answer
192
views
1
answer
... Hi I have downloaded a mass spec dataset from maxqb (http://maxqb.biochem.mpg.de/mxdb/).
I have then imported the data Into R specifying 0 values as NA (as I think this is correct for analysis using the Limma package):
exprs <- read_excel("exprs.xlsx", na="0")
I then normalise using norm ...
written 5 months ago by
reubenmcgregor88 • 0
• updated
5 months ago by
Gordon Smyth ♦ 38k
0
votes
1
answer
280
views
1
answers
... Thanks, yes, I want to plot a few heat maps with DE genes.
...
written 7 months ago by
reubenmcgregor88 • 0
0
votes
1
answer
280
views
1
answers
... Gordon, a related question I have (though happy to put it on a seperate thread if the question is too unrelated) is how to remove the effect of donors with this design?
My attempt was:
donor <- pData$donor
design_donor_effect <- model.matrix(~MV_only, data=pData)
y_batchremoved ...
written 7 months ago by
reubenmcgregor88 • 0
0
votes
1
answer
280
views
1
answers
... I was getting confused with other analyses I had done with the same dataset where I needed a contrast and wanted to use the same structure. Thank you for your help yet again Gordon! ...
written 7 months ago by
reubenmcgregor88 • 0
0
votes
1
answer
280
views
1
answers
... Thanks,
I did do that originally and tried to carry on but was not sure about how to then setup the contrast matrix.
currently the design looks like:
> head(design, 10)
(Intercept) donor4 donor8 MV_onlyother
Ao3 1 0 0 1
Ao8 1 0 ...
written 7 months ago by
reubenmcgregor88 • 0
3
votes
1
answer
280
views
1
answer
... I am using Limma to analyse some microarray data and have managed a simple workflow so far, but am struggling with a slightly more complex design matrix (despite trying to adapt some other answers on here to my question, sorry).
I have phenotypic data of an experiment that looks like this:
> he ...
written 7 months ago by
reubenmcgregor88 • 0
• updated
7 months ago by
Gordon Smyth ♦ 38k
0
votes
1
answer
301
views
1
answers
... Thank you Gordon,
Yes I had read that paper before posting and had an inkling that in hindsight control proteins would have been a good idea. ...
written 7 months ago by
reubenmcgregor88 • 0
2
votes
1
answer
301
views
1
answer
... I have been analysing protein array data with hundreds and thousands of proteins using Limma in R.
For normalisation I have been using the following:
y <- normalizeBetweenArrays(log2(exprs), method="quantile")
followed by box plots and density plots for QC. Followed by model fitting for d ...
written 7 months ago by
reubenmcgregor88 • 0
• updated
7 months ago by
Gordon Smyth ♦ 38k
0
votes
1
answer
383
views
1
answers
... Ok, understood I will look into Limmas normalisation procedures and QC etc and do it from there and then compare to the "who-knows-what company. Always good to check I guess.
Thank you for all the help
...
written 13 months ago by
reubenmcgregor88 • 0
0
votes
1
answer
383
views
1
answers
... Thanks. I see there is something I am not quite understanding. I am trying to understand the analysis in term of my experience with another package on RNAseq data where un-notmalised data is put in and normalised data is output by the model. I have asked for the raw expression, normalised values fro ...
written 13 months ago by
reubenmcgregor88 • 0
Latest awards to reubenmcgregor88
Supporter
7 months ago,
voted at least 25 times.
Scholar
2.0 years ago,
created an answer that has been accepted.
For A: Error in pcaplot3d from pcaExplorer, when running Deseq2 since update of package
Use of this site constitutes acceptance of our User
Agreement
and Privacy
Policy.
Powered by Biostar
version 16.09
Traffic: 258 users visited in the last hour