User: reubenmcgregor88

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Posts by reubenmcgregor88

<prev • 23 results • page 2 of 3 • next >
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(Closed) 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 linear model fittin ...
array R limma written 12 months ago by reubenmcgregor8840
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What values should I use for principle component analysis of microarray data?
... I have been doing a bit of reading about Principle Component Analysis (PCA) and have been using R to carry out PCA on some microarray data and have started with background subtracted raw fluorescent values. I can run PCA on any of the following datasets, each one giving different plots: 1) Unnorma ...
R pca microarray written 18 months ago by reubenmcgregor8840 • updated 18 months ago by Kevin Blighe53k
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Comment: C: What files should I ask for from protein array analysis, in order to carry out d
... Thanks, yes it will be more or less indistinguishable from microarray in many ways. Given that, my question is in order to import and use in Limma what should I ask for.My question is more about the terminology of what to ask for. I do not want to have to go through the normal QC and background su ...
written 18 months ago by reubenmcgregor8840
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What files should I ask for from protein array analysis, in order to carry out differential expression analysis? And which R package can I use?
... HI all, We have had some HuProt (protein microarrays) arrays done as well as some preliminary analysis done, giving fold changes and p-values for s simple case-control cohort. We would like to do some more detailed analysis based on further clinical data (such as stratify cases into acute and chro ...
protein-array R written 18 months ago by reubenmcgregor8840
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Does "the biostars handbook" contain sections on DNA, RNA and AA sequence alignment with phylogenetic tree construction?
... I have some experience, through teaching myself, of using R for RNAseq, ChIPseq etc, but have started in a new field of research. Specifically I am working with bacteria and would like to, for example, be able to align specific regions of AminoAcids (which is used to split the bacteria I am studying ...
biostars handbook written 2.0 years ago by reubenmcgregor8840
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Comment: C: annotatePeaks.pl Homer using "RNA"
... Sorry I meant to ask about annotatePeaks.pl not the motif searching, I have updated the post ...
written 2.4 years ago by reubenmcgregor8840
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annotatePeaks.pl Homer using "RNA"
... Hi all, I have successfully used the following function in Homer to annotate my peaks to closest genes: annotatePeaks.pl    > i.e. annotatePeaks.pl ERpeaks.txt hg18   > outputfile.txt My problem is that some of my peaks are in the middle of introns of genes but are being called to ...
homer chip-seq motif written 2.4 years ago by reubenmcgregor8840 • updated 18 months ago by CrisMar70
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Comment: C: ggplot2, point with border
... It is indeed (between ** below), which is why I am very confused at the random colour selection? vol + ggtitle(label = "Volcano Plot", subtitle = "Colored by fold-change direction") + geom_point(size = 2.5, alpha = 1, na.rm = T, shape=21, color = "black") + **scale_colour_m ...
written 2.4 years ago by reubenmcgregor8840
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Comment: C: ggplot2, point with border
... Thanks so much, This has made the following graph now, so colors and black surrounding working now: ![enter image description here][1] Sorry to be a pain, any idea why my color palette has been overwritten somehow? [1]: https://i.imgur.com/LgyfR7T.jpg > `vol <- ggplot(data, aes(x = lfc, ...
written 2.4 years ago by reubenmcgregor8840
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Comment: C: ggplot2, point with border
... Ah, gotcha. Thanks will remember this next time. ...
written 2.4 years ago by reubenmcgregor8840

Latest awards to reubenmcgregor88

Epic Question 9 months ago, created a question with more than 10,000 views. For ggplot2, point with border
Popular Question 12 months ago, created a question with more than 1,000 views. For annotatePeaks.pl Homer using "RNA"
Great Question 17 months ago, created a question with more than 5,000 views. For ggplot2, point with border
Popular Question 23 months ago, created a question with more than 1,000 views. For ggplot2, point with border

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