User: TitoPullo

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TitoPullo160
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United Kingdom
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5 years, 5 months ago
Joined:
6 years, 8 months ago
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Posts by TitoPullo

<prev • 27 results • page 1 of 3 • next >
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KEGG pathways associated to a gene using BiomaRt
... Hello, is there an easy way to get the get the list of KEGG pathways associated to a specific gene using biomaRt? I found a solution to retrieve the GO terms: https://www.biostars.org/p/1226/.. Is it possible use something similar for KEGG pathway terms? ...
pathways biomart kegg R written 5.4 years ago by TitoPullo160 • updated 4.9 years ago by sedaghat.nafiseh20
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David Output Interpretation
... I'm trying to understand bettern the output of an enrichment analysis done with DAVID . To each overrepresented term is associated a p-value and a Benjamini corrected p-value. Which one should be taken in account? It looks like that the Benjamini is the most correct one because it consider the multi ...
enrichment written 5.7 years ago by TitoPullo160 • updated 5.7 years ago by Devon Ryan92k
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Comment: C: Gene Disease (Cancer) Association
... I think PubMed is the best resource for me. ...
written 5.9 years ago by TitoPullo160
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Comment: C: Gene Disease (Cancer) Association
... But this website list all the studies involving that particular gene. It doesn't tell me if that gene is actually related with the disease. ...
written 5.9 years ago by TitoPullo160
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Gene Disease (Cancer) Association
... I'm a computer scientist, so I don't have a lot of knowledge about biology. I developed a statistical method to highlight some genes from microarray dataset. Now, I'd like to know if the gene I selected are related to the microarray problem. That is, given a microarray dataset about Prostate Cancer ...
gene association cancer disease function written 5.9 years ago by TitoPullo160
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What To Do With Null Gene Expression Level In Rna-Seq Analysis? Remove Them?
... I have a RNASeq dataset of 40K genes about 800 individuals. For many genes (around 30% of the total) the expression value is equal to 0 in almost every individual. I.e the expression level values for the Gene X is equal to 0 for 90% or 95% of the individuals. How should I deal with these Genes? Shou ...
gene expression rna microarray written 6.4 years ago by TitoPullo160 • updated 6.1 years ago by Biostar ♦♦ 20
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Calculate Linkage Disequilibrium For Snps (Using R^2)
... I have SNPs information for 500 individuals (samples). Given a SNP, for each individual is available the number of minor alleles measured in that sample (i.e 0,1 or 2). I need to calculate the linkage disequilibrium between each pair of SNPs. I've found this formula: where A (or B) and a (or b) ar ...
linkage snp written 6.4 years ago by TitoPullo160
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Comment: C: Snps Selection/Filtering
... Have you ever face with this problem (reduction of the number of SNPs)? If yes which approach did you used? ...
written 6.4 years ago by TitoPullo160
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Comment: C: Snps Selection/Filtering
... You're right, I made a mistake writing the post! Anyway is it a biologically correct approach? ...
written 6.4 years ago by TitoPullo160
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Snps Selection/Filtering
... I have a dataset with 2 Millions SNPs associated to 1000 individuals. Each SNP is represented, for each individual, as: 0,1 or 2 (the number of minor alleles). I'd like to reduce the number of SNPs in order to use them as attributes with an SVM. Is it a correct approach calculate the r^2 (r squared) ...
snp correlation selection filtering written 6.4 years ago by TitoPullo160

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