User: reubenmcgregor88

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Posts by reubenmcgregor88

<prev • 51 results • page 1 of 6 • next >
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Dealing with NA values from mass spec data using Limma, NA values.
... 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 ...
limma na mass spec written 9 months ago by reubenmcgregor880 • updated 9 months ago by Gordon Smyth39k
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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 10 months 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 10 months 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 10 months 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 10 months 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 10 months ago by reubenmcgregor880 • updated 10 months ago by Gordon Smyth39k
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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 11 months 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 11 months ago by reubenmcgregor880 • updated 11 months ago by Gordon Smyth39k
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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 17 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 17 months ago by reubenmcgregor880

Latest awards to reubenmcgregor88

Supporter 11 months ago, voted at least 25 times.
Scholar 2.3 years 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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