User: Mike Dewar

gravatar for Mike Dewar
Mike Dewar1.6k
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Location:
Columbia University, NYC, USA
Website:
http://www.columbia.ed...
Last seen:
9 years, 3 months ago
Joined:
9 years, 11 months ago
Email:
m*********@columbia.edu

I am a post-doc, looking at gene expression in CD8 T-Cell phenotypes. I'm interested in machine learning, specifically the application of latent variable modelling to the study of changing phenotypes.

Posts by Mike Dewar

<prev • 68 results • page 1 of 7 • next >
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Comment: C: Normalize Large Number Of Cel Files
... Seems like the consensus is "get a lot of RAM"! I shall have a go at abusing the computational resources open to me... Thanks for the help ...
written 9.3 years ago by Mike Dewar1.6k
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Comment: C: Normalize Large Number Of Cel Files
... oops - I've updated the link. The group of arrays is from the Immunological Genome Project ...
written 9.3 years ago by Mike Dewar1.6k
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Normalize Large Number Of Cel Files
... I'm trying to normalize a set of 508 CEL files, available on GEO: http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE15907 I've been trying to use the R package aroma affymetrix: http://www.aroma-project.org/ to achieve this, but it's randomly crashing with strange errors. The benefit of the a ...
R bioconductor written 9.3 years ago by Mike Dewar1.6k • updated 9.3 years ago by Markus Schmidberger0
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Comment: C: Affy Probeset Names
... thanks! I've checked the RefSeq property matches up between the common probesets in each library but not the actual sequences. How would I access the sequences, independently of the annotations? ...
written 9.6 years ago by Mike Dewar1.6k
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Affy Probeset Names
... I'm interested in comparing data from two chips - one is a hgu133plus2 chip and the other is an older hgu133a chip. From the manufacturer's website, it states that the newer chip is the "Human Genome U133 Set plus 6,500 additional genes". Looking at the annotations from bioconductor, I get the follo ...
microarray affymetrix written 9.6 years ago by Mike Dewar1.6k • updated 9.6 years ago by Shigeta160
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Comment: C: R: Topgo Usage Question
... I didn't want to complain, but I think maybe the topGO documentation is a little confusing. Following the example mentioned by Khader, I've constructed allGenes as a factor, indicating which genes I'm interested in, and it seems to work. The subsequent Fisher test seems to be giving me sensible resu ...
written 9.6 years ago by Mike Dewar1.6k
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Answer: A: R: Topgo Usage Question
... By cobbling together both responses, and the link suggested by Khader, it turns out that this is all I need: library(topGO) library(mogene10sttranscriptcluster.db) # exprset is an Expression Set object # interesting_genes are the probesets I'd like to perform GO Enrichment on # ...
written 9.7 years ago by Mike Dewar1.6k • updated 7 months ago by RamRS26k
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Comment: C: R: Topgo Usage Question
... @Khader - thanks! That provided the clues I needed. It turns out that I was maybe making life a bit more complicated than necessary. Shall I put what I did in the end as answer, or just delete the question? I guess this turned out to be a bit more of a Bioconductor mailing list question... ...
written 9.7 years ago by Mike Dewar1.6k
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Comment: C: R: Topgo Usage Question
... Despite the two helpful answers from Brad and lGautier below, I still can't get this guy to work. It's starting to feel more like a Bioconductor list question now, though. ...
written 9.7 years ago by Mike Dewar1.6k
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Comment: C: R: Topgo Usage Question
... Despite the two helpful answers below, I still can't get this guy to work. It's starting to feel more like a Bioconductor list question now, though. ...
written 9.7 years ago by Mike Dewar1.6k

Latest awards to Mike Dewar

Supporter 9.3 years ago, voted at least 25 times.
Guru 9.3 years ago, received more than 100 upvotes.
Autobiographer 9.3 years ago, has more than 80 characters in the information field of the user's profile.
Popular Question 9.3 years ago, created a question with more than 1,000 views. For Normalize Large Number Of Cel Files
Appreciated 9.3 years ago, created a post with more than 5 votes. For Normalize Large Number Of Cel Files
Good Question 9.3 years ago, asked a question that was upvoted at least 5 times. For Normalize Large Number Of Cel Files
Student 9.3 years ago, asked a question with at least 3 up-votes. For Normalize Large Number Of Cel Files
Good Question 9.6 years ago, asked a question that was upvoted at least 5 times. For Affy Probeset Names
Teacher 9.7 years ago, created an answer with at least 3 up-votes. For A: R: Topgo Usage Question
Student 9.8 years ago, asked a question with at least 3 up-votes. For Levels Of Gene Homologous-Ness?
Appreciated 9.8 years ago, created a post with more than 5 votes. For Levels Of Gene Homologous-Ness?
Good Question 9.8 years ago, asked a question that was upvoted at least 5 times. For Levels Of Gene Homologous-Ness?
Popular Question 9.8 years ago, created a question with more than 1,000 views. For Levels Of Gene Homologous-Ness?
Teacher 9.8 years ago, created an answer with at least 3 up-votes. For A: T Cell Specific Gene Expression Data
Student 9.9 years ago, asked a question with at least 3 up-votes. For Homology + Bioconductor
Appreciated 9.9 years ago, created a post with more than 5 votes. For Homology + Bioconductor
Popular Question 9.9 years ago, created a question with more than 1,000 views. For Homology + Bioconductor

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