User: Ankur

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Ankur100
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Posts by Ankur

<prev • 8 results • page 1 of 1 • next >
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Comment: C: Finding All The Genes That Are In A Given Set Of Genomic Co-Ordinates Using R
... The trouble though is that I've got a dataframe full of segments and samples and I need to apply that function to each row so I can get a vector of gene symbols for each row; biomaRt doesn't seem to be very good at doing that. ...
written 6.0 years ago by Ankur100
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Finding All The Genes That Are In A Given Set Of Genomic Co-Ordinates Using R
... Hi, So I've got a list of chromosome segments amplified and deleted by sample with the chromosome, start and end co-ordinates. How can I, using R, get hold of identifiers for all the genes that fall within those segments? Cheers. ...
R cnv written 6.0 years ago by Ankur100 • updated 6.0 years ago by Steve Lianoglou5.0k
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Finding Out How Many Times A Particular Nucleotide Sequence Recurs In The Exome.
... So I'm trying to figure out how many instances of given trinucleotide sequences are present in the human exome for purposes of enrichment analysis...what is the best way to do this? ...
nucleotide sequence analysis written 6.2 years ago by Ankur100 • updated 3.2 years ago by Biostar ♦♦ 20
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Comment: C: Retreiving Data From Tcga Database
... the cBio portal for cancer genomics enables you to do just that. ...
written 6.2 years ago by Ankur100
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Answer: A: Normalising Arrays Across Multiple Datasets For Unsupervised Clustering.
... I did find a possible solution though - given that my arrays are all of a single Affymetrix platform I will be able to apply frozen RMA normalisation to facilitate direct comparison. ...
written 6.4 years ago by Ankur100
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Comment: C: Normalising Arrays Across Multiple Datasets For Unsupervised Clustering.
... I've used microarray meta-analysis before in a different setting but the fundamental caveat is that those tend to be supervised analyses, with the P.values et cetera being generated in relation to normal tissue, for instance, whereas I'm looking to use unsupervised clustering here in this case to di ...
written 6.4 years ago by Ankur100
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Normalising Arrays Across Multiple Datasets For Unsupervised Clustering.
... Hi there! I'm interested in using multiple datasets consisting of arrays from the same type of cancer to check for the presence of molecular subtypes. What is the best way by which I can normalize all the arrays so they become comparable before I run consensus clustering? Combat + rma? Cheers, An ...
array normalization classification written 6.4 years ago by Ankur100
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Workflows For Microarray Meta-Analysis Projects.
... Hi everyone. I have been contemplating doing a few analyses of publicly available affy array data using R and Bioconductor to define signatures for phenotypes/identify transcriptional biomarkers et cetera. I always work using raw data and the options I have in terms of workflows are [1] Pool toget ...
R workflow bioconductor microarray written 6.9 years ago by Ankur100 • updated 6.9 years ago by boczniak767680

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