User: reubenmcgregor88
reubenmcgregor88 • 40
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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 linear model fittin ...
written 12 months ago by
reubenmcgregor88 • 40
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... 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 ...
written 18 months ago by
reubenmcgregor88 • 40
• updated
18 months ago by
Kevin Blighe ♦ 53k
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... 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
reubenmcgregor88 • 40
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... 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 ...
written 18 months ago by
reubenmcgregor88 • 40
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... 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 ...
written 2.0 years ago by
reubenmcgregor88 • 40
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... Sorry I meant to ask about annotatePeaks.pl not the motif searching, I have updated the post ...
written 2.4 years ago by
reubenmcgregor88 • 40
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... 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 ...
written 2.4 years ago by
reubenmcgregor88 • 40
• updated
18 months ago by
CrisMar • 70
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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
reubenmcgregor88 • 40
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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
reubenmcgregor88 • 40
0
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17k
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Comment:
C: ggplot2, point with border
... Ah, gotcha.
Thanks will remember this next time. ...
written 2.4 years ago by
reubenmcgregor88 • 40
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