User: phil.chapman

gravatar for phil.chapman
phil.chapman120
Reputation:
120
Status:
Trusted
Location:
United Kingdom
Last seen:
5 months, 3 weeks ago
Joined:
1 year, 12 months ago
Email:
p***********@cruk.manchester.ac.uk

I am Lead Scientist for Bioinformatics in the Drug Discovery Unit at the Cancer Research UK Manchester Institute. 

Posts by phil.chapman

<prev • 23 results • page 1 of 3 • next >
0
votes
2
answers
257
views
2
answers
Comment: C: Focal stacking of images in R/EBImage
... Thanks Bernd!  So you're just taking the maximum intensity for each pixel? ...
written 8 months ago by phil.chapman120
0
votes
3
answers
233
views
3
answers
Answer: A: Processing imaging data from high throughput compound screen with EBImage
... Some other useful links for posterity: Earl Glynn's RNotes blog: http://earlglynn.github.io/RNotes/package/EBImage/index.html Slideset from Wolfgang Huber: http://mlpm.eu/static/media/uploads/mlpm13_slides_huber01.pdf Machine Learning in cell biology - teaching computers to read phenotypes: http: ...
written 8 months ago by phil.chapman120
3
votes
2
answers
257
views
2
answers
Focal stacking of images in R/EBImage
... Has anyone got experience of carrying out a focal stacking operation on an image stack in R?  This is where one has a series of images with the same field of view but different focal planes, and these are combined into a single image where everything is magically in focus.  Thanks, Phil ...
ebimage written 8 months ago by phil.chapman120 • updated 8 months ago by Bernd Fischer540
0
votes
3
answers
233
views
3
answers
Comment: C: Processing imaging data from high throughput compound screen with EBImage
... This is great thanks Andrzej! ...
written 9 months ago by phil.chapman120
0
votes
3
answers
233
views
3
answers
Comment: C: Processing imaging data from high throughput compound screen with EBImage
... Thanks Wolfgang this is exactly the sort of information I was hoping for. My main issue to start with is how to get the image data out of the commercial software (Perkin Elmer Opera Phenix) in the first place and into an open format.  I naively assumed it would just be a bunch of images but it seem ...
written 9 months ago by phil.chapman120
7
votes
3
answers
233
views
3
answers
Processing imaging data from high throughput compound screen with EBImage
... Hi, My group are planning to conduct a 15k compound high content biology screen and I'm looking into options for analysing the image data.  We'd probably just be doing a simple cell count and maybe cell size to start with.  Although we have commerical software to do this (Definiens), I'm not sure h ...
ebimage written 9 months ago by phil.chapman120
0
votes
2
answers
200
views
2
answers
Answer: A: Extract GRanges for gene data frame
... I'm not sure if you're trying to end up with a data.frame or a GRanges object but either way you might be better off coercing to/from a data frame as it makes the join operation easier. For example: library(EnsDb.Hsapiens.v75) library(GenomicRanges) library(dplyr) library(tibble) #info on genes g ...
written 10 months ago by phil.chapman120
0
votes
2
answers
418
views
2
answers
Answer: A: Labeling points with hgnc symbols on the MA plot in DESeq2
... Or if you fancy a visit to the tidyverse then this is the equivalent: library(DESeq2) library(ggplot2) library(dplyr) library(ggrepel) set.seed(25) dds <- makeExampleDESeqDataSet() dds <- DESeq(dds) res <- results(dds, tidy=TRUE) res$Symbol <- paste0("Symbol", 1:1000) res_df <- res ...
written 11 months ago by phil.chapman120
0
votes
2
answers
264
views
2
answers
Answer: A: most efficient way to read adjacency matrix to make networkd3 graph
... It's quite difficult to follow your code without being able to run it.  As I understand it you're starting from a matrix, so perhaps you could make a very small, toy object that you could include in your code to get us started?  The following approach may be useful as it generates an R command at th ...
written 11 months ago by phil.chapman120
0
votes
1
answers
232
views
1
answers
Answer: A: Meta analysis of healthy and diseased data using illumina microarrays
... I think in this situation the best approach is to normalise together and do the analysis, but when reporting the results back give a very clear caveat that there's a batch effect that it's impossible to correct for that may confound the results.  How much of an issue this is will depend on the size ...
written 12 months ago by phil.chapman120

Latest awards to phil.chapman

Autobiographer 12 months ago, has more than 80 characters in the information field of the user's profile.
Scholar 14 months ago, created an answer that has been accepted. For A: Meta analysis of healthy and diseased data using illumina microarrays

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.2.0
Traffic: 364 users visited in the last hour