User: marion.ryan

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marion.ryan40
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Posts by marion.ryan

<prev • 14 results • page 1 of 2 • next >
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random forest advice
... I am using random forest package to predict 'norm' versus 'chol', with the code below and have got a nice output regarding the importance of a panel of genes contributing to the classification of diseased tissues however I have been reading up on this and am wondering if I need a training and tes ...
randomforest geneexpression written 5 months ago by marion.ryan40
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Comment: A: Predictive model from gene expression profile of diseased samples
... Thank you so Kevin much for that information, its a great suggestion and more specific to what I am trying to achieve. I was getting very bogged down in the amount of information and tools out there as my data set is very simple, glad I asked. Thanks again Marion ...
written 5 months ago by marion.ryan40
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Predictive model from gene expression profile of diseased samples
... Hello, I am looking for some advice. I have 18 diseased tissue's, 11 normal and 21 DE genes. I want to find the best predictors of disease using these genes. If anyone has any experience of predictive models, I would be interested in the processes and any caveats and also some useful visualization ...
prediction R svm gene expression nanostring written 5 months ago by marion.ryan40 • updated 5 months ago by Biostar ♦♦ 20
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Visualisation of SVM used to classify disease states from nanostring data
... I have a data set of normalised expression values from NanoString for two disease states. I have generated an SVM object within library(e1071), and I have no idea how to visualise it. 29 observations of 36 variables (gene expression) and two states (normal (11) and diseased 18)) -first column. Any d ...
R svm nanostring written 6 months ago by marion.ryan40 • updated 6 months ago by GenoMax96k
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Comment: C: haploview to cervus
... Thank you so much that is a real help, I'll just work on formatting a subset of SNPs (Haploview wants has the genotypes in one column as opposed to two) for and see if it works on that basis. I might check out Plink also. M :) ...
written 15 months ago by marion.ryan40
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Comment: A: haploview to cervus
... It appears to be still in use (licenced 2014), Its not terribly good at describing the format it needs but calls it a genotype file which it describes with words, I have mine in haploview format and I am wondering if ther is a quick was of changing this format http://www.fieldgenetics.com/pages/abou ...
written 15 months ago by marion.ryan40
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haploview to cervus
... I have formatted a genotype file for haploview and have now obtained the genotypes of the parents and wish to carry out parentage testing (Sheep). Any advise on converting my existing file format so it would be suitable for analysis in Cervus or any other parentage testing software, would be greatly ...
parentage software snp written 15 months ago by marion.ryan40
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Comment: A: RS numbers to VCF format -sheep genome
... All done! Thank you so much. Marion ...
written 2.1 years ago by marion.ryan40
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RS numbers to VCF format -sheep genome
... Hello, I would like to retrieve information in VCF format using a list of RS numbers for Sheep genome, easiest solution possible please!! Marion ...
vcf rs snp written 2.1 years ago by marion.ryan40
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Comment: A: VCF SNP analysis
... Thanks for the quick answers, I am looking for the best tool with which to navigate and explore the VCF files derived from an RNAseq experiment in order to obtain specific SNPs relating to particular genes and also compare the samples in relation to specific SNPs, so any tips in relation to the best ...
written 2.8 years ago by marion.ryan40

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