User: reubenmcgregor88
reubenmcgregor88 • 0
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Posts by reubenmcgregor88
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... 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 3 months ago by
reubenmcgregor88 • 0
• updated
3 months ago by
Gordon Smyth ♦ 37k
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... Thanks, yes, I want to plot a few heat maps with DE genes.
...
written 5 months ago by
reubenmcgregor88 • 0
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... 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 5 months ago by
reubenmcgregor88 • 0
0
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... 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 5 months ago by
reubenmcgregor88 • 0
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... 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 5 months ago by
reubenmcgregor88 • 0
3
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... 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 5 months ago by
reubenmcgregor88 • 0
• updated
5 months ago by
Gordon Smyth ♦ 37k
0
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... 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 5 months ago by
reubenmcgregor88 • 0
2
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... 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 5 months ago by
reubenmcgregor88 • 0
• updated
5 months ago by
Gordon Smyth ♦ 37k
0
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... 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 11 months ago by
reubenmcgregor88 • 0
0
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... 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 11 months ago by
reubenmcgregor88 • 0
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22 months ago,
created an answer that has been accepted.
For A: Error in pcaplot3d from pcaExplorer, when running Deseq2 since update of package
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