User: Daniel Brewer

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Daniel Brewer1.9k
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Posts by Daniel Brewer

<prev • 182 results • page 2 of 19 • next >
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Comment: C: Best way to get updated annotation for BACs
... That's great, many thanks for that. The only problem I am having is that some of the clones do not come up in the bacEndPairs table, for example RP11-363L4 or CTD-2001A18. When I search for these in Ensembl they sometimes are there as a sequence, but sometimes not. Any ideas? The non-matching clon ...
written 8.8 years ago by Daniel Brewer1.9k
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Best way to get updated annotation for BACs
... Hello, I am dealing with a BACs microarray, but the annotation I have is from an old version of the human genome. Could anyone suggest some ways of updating the information to hg19? I would initially like the positional information, but also want gene(s) the BAC covers and whether the BAC covers ...
microarray annotation cancer bac written 8.8 years ago by Daniel Brewer1.9k • updated 8.8 years ago by Sean Davis21k
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GEOquery: Best way to get a phenodata table from GSE
... Hello, For a particular GSE set I have downloaded all the raw data but I would like to be able to extract all the phenodata associated with each sample into a table so I can use it in the analysis. 4.1 of the manual shows a way of getting what I want but I would have to download the whole GSE matr ...
cancer written 8.8 years ago by Daniel Brewer1.9k • updated 8.8 years ago by Sean Davis21k
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Sources of information about amplified genes in cancer
... Hello, I was wondering whether anyone could suggest sources of information about amplified genes in cancer, especially if the website tries to combine it with (over)expression information. We wrote a review on amplified and expressed genes recently and are trying to get a sense of what else is out ...
cancer written 8.9 years ago by Daniel Brewer1.9k
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Genecards v3 access
... Hello, Just wondering if there was a way to interrogate genecards v3 from within bioconductor/R? Thanks Dan -- ************************************************************** Daniel Brewer, Ph.D. Institute of Cancer Research Molecular Carcinogenesis Email: daniel.brewer at icr.ac.uk ************* ...
cancer written 8.9 years ago by Daniel Brewer1.9k • updated 8.9 years ago by Sean Davis21k
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Comment: C: Machine learning, cross validation and gene selection
... Many thanks for the detailed reply. That is very informative. What I mean by optimal is the collection of genes that any further studies should use. For example, say I have a cancer/normal dataset and I want to find the top 10 genes that will classify the tumour type according to an SVM. I would ...
written 9.0 years ago by Daniel Brewer1.9k
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Machine learning, cross validation and gene selection
... Hello, I am getting a bit confused about gene selection and machine learning and I was wondering if you could help me out. I have a dataset that is classified into two groups and my aim is to get a small number of genes (10-20) in a gene signature that I will in theory be able to apply to over dat ...
go cancer written 9.0 years ago by Daniel Brewer1.9k • updated 9.0 years ago by Vincent J. Carey, Jr.6.3k
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Answer: A: Biobase: How to replace the ExpressionSet phenoData?
... Don't worry I had a typo. Ooops. On 25/08/2010 10:58 AM, Daniel Brewer wrote: > Hello, > > I have an ExpressionSet object (nodups) and I would like to replace its > phenoData with a different data.frame object (pdata). I cannot work out > how to do it. I have tired: > >> ...
written 9.0 years ago by Daniel Brewer1.9k
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Biobase: How to replace the ExpressionSet phenoData?
... Hello, I have an ExpressionSet object (nodups) and I would like to replace its phenoData with a different data.frame object (pdata). I cannot work out how to do it. I have tired: > phenoData(nodups) <- new("AnnotatedDataFrame",pData) Error in value[[3L]](cond) : AnnotatedDataFrame 'data' ...
cancer written 9.0 years ago by Daniel Brewer1.9k
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Comment: C: xps: root.profile on a asubset of the data
... Dear Christian, Many thanks for making some code changes, thats great. Unfortunately I have tried it and it doesn't seem to work. I create a list of the tree nodes: > samples <- unlist(treeNames(rootData)) Then check to see if I can use the root graphics: > root.image(rootData,treename ...
written 9.0 years ago by Daniel Brewer1.9k

Latest awards to Daniel Brewer

Centurion 7.6 years ago, created 100 posts.
Popular Question 7.6 years ago, created a question with more than 1,000 views. For Gene symbol to KEGG gene ids
Popular Question 7.6 years ago, created a question with more than 1,000 views. For Correlation matrix and pca on matrix with NA values
Popular Question 7.6 years ago, created a question with more than 1,000 views. For Filtering before differential expression analysis of microarrays - New paper out
Popular Question 7.6 years ago, created a question with more than 1,000 views. For Genecards v3 access
Popular Question 7.6 years ago, created a question with more than 1,000 views. For Limma: Contrasts comparing one factor to multiple others
Popular Question 7.6 years ago, created a question with more than 1,000 views. For Gene symbol to KEGG gene ids
Popular Question 7.6 years ago, created a question with more than 1,000 views. For Agilent 4x44k annotation file
Popular Question 7.6 years ago, created a question with more than 1,000 views. For Visualise KEGG pathway and highlight genes
Popular Question 7.6 years ago, created a question with more than 1,000 views. For Limma and logistic regression
Popular Question 7.6 years ago, created a question with more than 1,000 views. For quantile normalization of one dataset to another
Popular Question 7.6 years ago, created a question with more than 1,000 views. For Finding genes with significant linear regression or trend
Great Question 7.6 years ago, created a question with more than 5,000 views. For Correlation matrix and pca on matrix with NA values

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