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User: reubenmcgregor88

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Posts by reubenmcgregor88

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Comment: C: Limma analysis, controlling for Donors.
... Thanks, yes, I want to plot a few heat maps with DE genes. ...
written 4 weeks ago by reubenmcgregor880
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Comment: C: Limma analysis, controlling for Donors.
... 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 4 weeks ago by reubenmcgregor880
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Comment: C: Limma analysis, controlling for Donors.
... 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 4 weeks ago by reubenmcgregor880
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Comment: C: Limma analysis, controlling for Donors.
... 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 4 weeks ago by reubenmcgregor880
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Limma analysis, controlling for Donors.
... 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 ...
microarray limma R written 4 weeks ago by reubenmcgregor880 • updated 4 weeks ago by Gordon Smyth36k
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Comment: C: Array Normalization on focussed array in Limma using R
... 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 weeks ago by reubenmcgregor880
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Array Normalization on focussed array in Limma using R
... 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 ...
microarray limma R written 5 weeks ago by reubenmcgregor880 • updated 5 weeks ago by Gordon Smyth36k
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Comment: C: Am I on the right tracks with a 3 factor design in Limma?
... 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 7 months ago by reubenmcgregor880
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Comment: C: Am I on the right tracks with a 3 factor design in Limma?
... 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 7 months ago by reubenmcgregor880
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Comment: C: Am I on the right tracks with a 3 factor design in Limma?
... I feel like I will be apologising allot if I'm not careful, I will be next time, sorry. I changed all me phenotypic data half way through writing the post as I realised some of my nomenclature was too long winded so I originally had control_NA which I replaced with na, I have updated the post to r ...
written 7 months ago by reubenmcgregor880

Latest awards to reubenmcgregor88

Supporter 5 weeks ago, voted at least 25 times.
Scholar 18 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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