User: Davide Chicco

gravatar for Davide Chicco
Davide Chicco110
Reputation:
110
Status:
Trusted
Location:
Canada
Website:
http://www.davidechicc...
Last seen:
5 months, 3 weeks ago
Joined:
8 years, 2 months ago
Email:
d************@gmail.com

Posts by Davide Chicco

<prev • 36 results • page 1 of 4 • next >
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Answer: A: How to retrieve the genes associated to an RNA PAXgene gene expression dataset f
... I was able to solve my own problem by just checking the getGEO() function: I realized that the getGPL must be set to TRUE. if (!requireNamespace("BiocManager", quietly = TRUE)) install.packages("BiocManager") BiocManager::install() BiocManager::install("GEOquery") ...
written 5 months ago by Davide Chicco110
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Comment: C: How to retrieve the genes associated to an RNA PAXgene gene expression dataset f
... Thanks Kevin. I saw that page but I cannot understand how to access those data header fields. Do you know how I can do that? ...
written 5 months ago by Davide Chicco110
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How to retrieve the genes associated to an RNA PAXgene gene expression dataset from GEO?
... In the past I have been working with a [gene expression dataset][1] generated with Affymetrix and I was able to use the getBM() Bioconductor function to retrieve the genes associated to it. These are the lines of R code I used to use: # Gene list mart <- useMart("ENSEMBL_MART_ENSEMBL") ...
geo r-language rna rna-seq written 5 months ago by Davide Chicco110
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Comment: C: Differential gene expression analysis of real-valued expression data of genes an
... Thank you guys for your replies. There's a lot of material online and I feel like I am drowning in it. I found [this interesting question and answer here on BioStars.org][1], that I tried to implement for my case. I used `lmFit(table)` and `eBayes(fit)`, as explained, without `design`. I was able t ...
written 10 months ago by Davide Chicco110
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Comment: C: Differential expression using microarray data and limma, where am I going wrong?
... Very interesting thread. I am new to differential gene expression and would like to understand more about it. In this case, what is the meaning of the p-value of each gene generated by the limma model? Thanks! ...
written 10 months ago by Davide Chicco110
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Differential gene expression analysis of real-valued expression data of genes and individuals
... Hi I've a dataset of gene expressions of 102 patients and 9 healthy controls. I downloaded this [dataset from GEO][1], I applied several preprocessing steps (normalization, batch correction based on date, etc), and I was finally able to generate a table containing: - the individuals on the rows - ...
rna gene-expression gen-expression rna-seq written 10 months ago by Davide Chicco110 • updated 10 months ago by h.mon29k
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How to validate the association between a ranked list of genes found computationally and a disease?
... Hi all I applied some bioinformatics methods to retrieve the genes related to a cohort of patients having a particular disease and to a cohort of healthy controls. I then applied some biostatistics and machine learning techniques to rank all the genes based on their importance/significance in rela ...
gene diseases validation written 10 months ago by Davide Chicco110
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Comment: C: bcftools / samtools, which database does the MAF function use?
... Hi Pierre Thanks for the reply. Are you saying the information about if a variant is rare (or not) is present in the header of the VCF file we're using? If yes, how does bcftools view retrieve it? And, more important, how can we know which database did the people who generated the file used to st ...
written 12 months ago by Davide Chicco110
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bcftools / samtools, which database does the MAF function use?
... Hi I am working with `bcftools view` to [filter variants][1] based on a specific MAF (minor allele frequency) cutoff. It works well but there's an information I am missing: which database is bcftools using to apply the MAF filter, that is to claim if a variant is rare or not? Thanks! -- Davide ...
maf bcftools samtools written 12 months ago by Davide Chicco110 • updated 12 months ago by Pierre Lindenbaum127k
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Comment: C: How to check the presence of mutations of a specific gene in a specific VCF file
... Hi Erin_Ensembl another question: I am exploring VEP; how are non-synonymous variants labeled in a typical VEP output? I see many biotypes (nonsense_mediated_decay, protein_coding, retained_intron, etc) but I cannot understand if one is suitable for me. Thanks! ...
written 12 months ago by Davide Chicco110

Latest awards to Davide Chicco

Appreciated 9 months ago, created a post with more than 5 votes. For Affymetrix Gene Id Format - What Does "At" Stand For?
Great Question 9 months ago, created a question with more than 5,000 views. For Affymetrix Gene Id Format - What Does "At" Stand For?
Popular Question 5.4 years ago, created a question with more than 1,000 views. For Affymetrix Gene Id Format - What Does "At" Stand For?
Popular Question 8.2 years ago, created a question with more than 1,000 views. For Affymetrix Gene Id Format - What Does "At" Stand For?
Student 8.2 years ago, asked a question with at least 3 up-votes. For Affymetrix Gene Id Format - What Does "At" Stand For?

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