User: Daniel Brewer

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Daniel Brewer1.8k
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Posts by Daniel Brewer

<prev • 182 results • page 1 of 19 • next >
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RMA normalisation of test microarray data to training data
... Hello, We have done some analysis on a set of Affy microarray data normalised by RMA and produced a predictor. We would like to test this predictor on a training set we have. Is it possible to RMA normalise the test dataset so that the probes have the same distribution as the training dataset wit ...
microarray go cancer affy written 5.9 years ago by Daniel Brewer1.8k • updated 5.9 years ago by James W. MacDonald45k
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Comment: C: Minimal region of overlap between two GRanges objects
... Thanks Martin, Yes you're right a simple intersect works great. I had a suspicion I was missing something very obvious. Many thanks. Dan On 13 Dec 2011, at 4:49 PM, Martin Morgan wrote: > On 12/13/2011 07:00 AM, Daniel Brewer wrote: >> Dear mailing list, >> >> I have two G ...
written 5.9 years ago by Daniel Brewer1.8k
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Minimal region of overlap between two GRanges objects
... Dear mailing list, I have two GRanges objects each containing segments of copy number change for a tumour. I would like to find regions where there is copy number change in both the tumours. I though findOverlaps was giving me what I wanted but soon found that findOverlaps(A,B) != findOverlaps(B, ...
cancer written 5.9 years ago by Daniel Brewer1.8k • updated 5.9 years ago by Martin Morgan ♦♦ 20k
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Bioinformatics/biostatistics position at the Institute of Cancer Research, UK
... JOB TITLE: Biostatistican LOCATION: The Institute of Cancer Research, Sutton SECTION & TEAM: Division of Genetics and Epidemiology, Molecular Epidemiology Team SALARY RANGE: ?27,536 to ?38,225 per annum CONTRACT: Full time for 2 years, from 9th of January 2012 JOB SUMMARY: This post forms part ...
sequencing microarray genetics cancer written 6.1 years ago by Daniel Brewer1.8k
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Answer: A: Average based on group
... Hi Fabrice, Check out the library plyr and in particular the function ddply(), which will do exactly what you want. There are also various in built functions to do this kind of thing but the results aren't as sensible as with ddply. Dan *********************************************************** ...
written 6.5 years ago by Daniel Brewer1.8k
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UK Beginner bioconductor courses
... Hello, There is someone in the lab with no R or programming experience that would like to start using bioconductor. Is there any courses suitable in the UK in the next few months? I have had a web search but couldn't find anything suitable. Many thanks Dan -- ********************************** ...
cancer written 6.6 years ago by Daniel Brewer1.8k • updated 6.6 years ago by Manikhandan V A40
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Normalising to Agilent controls in a two-colour experiment
... Hello, I am currently working on a rather strange project where amoeba along with a human cell line have been hybridised to an Agilent 4x44k microarray. As I wouldn't expect the majority of probes for the amoeba sample to be expressed, the assumption for LOESS that on average there isn't any diffe ...
cancer written 6.6 years ago by Daniel Brewer1.8k
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Limma: design for a multiple level factor taking into account centre and plate
... Hello, We have a microarray dataset where there seems to be significant variation caused by the centre (2 centres) the sample came from and the plate (2 plates), so I would like to basically remove these effects by including them in the linear model for any other comparison I do. I have a factor s ...
microarray cancer written 7.0 years ago by Daniel Brewer1.8k
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Comment: C: Best way to get updated annotation for BACs
... Hello, Sorry to come back onto this, but I can't get Lift Genome Annotations (http://genome.ucsc.edu/cgi-bin/hgLiftOver) to work whatever I do. Has anyone else had any success with this tool? I always get "#Deleted in new" for all the Clone's positions. In fact, even if I try a test like "Chr1:100 ...
written 7.1 years ago by Daniel Brewer1.8k
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Comment: C: Best way to get updated annotation for BACs
... On 03/11/2010 5:11 PM, Sean Davis wrote: > Do you have the original design file with genomic locations? If so, use > the UCSC liftover tool to go from the old genome to the genome of your > choice. Have the arrays been used in a published experiment? If so, > the design file may be ...
written 7.1 years ago by Daniel Brewer1.8k

Latest awards to Daniel Brewer

Popular Question 5.9 years ago, created a question with more than 1,000 views. For Correlation matrix and pca on matrix with NA values
Popular Question 5.9 years ago, created a question with more than 1,000 views. For Gene symbol to KEGG gene ids
Centurion 5.9 years ago, created 100 posts.

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