User: ioantika

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ioantika10
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2 years, 3 months ago
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Posts by ioantika

<prev • 10 results • page 1 of 1 • next >
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Comment: C: Calculate AU p-value of the first division in R pvrect function
... 1. The percentages range from 0.00 to 1.00. I was informed that correlation in distance, along with ward.D2 in cluster method was suitable for that kind of data. 2. I know, I just need a metric in the form of AU/BP or anything else in terms of statistical tests to report that the first two clusters ...
written 15 months ago by ioantika10
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Calculate AU p-value of the first division in R pvrect function
... I was recently investigating hierarchical cluster analysis algorithms using multiscale bootstrap resampling and would like to ask the following questions regarding one case of mine, using R package 'pvclust' 1. What are the best options for Distance (default;correlation) and Cluster method (de ...
R next-gen sequencing written 15 months ago by ioantika10 • updated 15 months ago by Jean-Karim Heriche15k
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Comment: C: Connection timeout when using multiple commands on eutils
... Yes! Any suggestions welcome. ...
written 23 months ago by ioantika10
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Connection timeout when using multiple commands on eutils
... I have successfully constructed a series of functions based on `eutils` that capture the rsID of a given SNP as a character variable and search for clinical significance strings on clinVAR and dbSNP. When I run every function with `apply()` on a column of >1000 whole exome sequencing entries I us ...
software error R snp written 23 months ago by ioantika10 • updated 23 months ago by Newgene340
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Comment: C: SciClone not numeric error
... I don't have copy numbers, just SNPs. I tried lowering down minimumDepth but I get the same results. My files contain 7-300 rows of SNP data for all sites per patient (primary, metastatic, normal) and I really want to get it working before the ESMO submission deadline. ...
written 2.2 years ago by ioantika10
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Comment: C: SciClone not numeric error
... Although the test files work just fine my actual patient data give me "Error in kmeans(X, N.c, nstart = 1000) : more cluster centers than distinct data points." I've tried header=FALSE and still the same. ...
written 2.2 years ago by ioantika10
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Comment: C: SciClone not numeric error
... I tried the as.numeric solution and it turns out that all values in V3, V4, and V5 are converted in irrelevant/random numbers. My VAFs are expressed as percentages (%) with 4 after comma values eg. 18,4587% ...
written 2.2 years ago by ioantika10
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SciClone not numeric error
... I tried to use sciClone on test data prior to applying any script on my actual patient database, but the program persistently keeps returning the following error message; > [1] "checking input data..." [1] "No copy number files specified. > Assuming all variants have a CN of > 2." [1] "ERR ...
genome R next-gen snp written 2.2 years ago by ioantika10 • updated 2.2 years ago by Chris Miller19k
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How to predict the effect of 3UTR SNPs on miRNA docking and polyadenylation
... I am particularly interested for rs11515 and rs1137282, in terms of the possible effects for polyadenylation and interaction with miRNAs. I would appreciate any machine learning/bioinformatics approach that is being used widely, despite the fact that I haven't found it already. ...
next-gen snp polyadenylation mirna written 2.2 years ago by ioantika10 • updated 2.2 years ago by Biostar ♦♦ 20
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How to integrate dbSNP data with my database?
... For some odd reason, the bioinformatics team responsible for providing me with NGS data records only heterozygous and homozygous to the opposite of the reference allele. That means that patient identification numbers are sometimes recorded with the major allele only and therefore lose the homozygous ...
next-gen dbsnp snp sequencing written 2.3 years ago by ioantika10 • updated 2.3 years ago by Pierre Lindenbaum108k

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