User: Davide Chicco

gravatar for Davide Chicco
Reputation:
90
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Trusted
Location:
Canada
Website:
http://www.davidechicc...
Last seen:
1 week, 2 days ago
Joined:
7 years, 9 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 9 days ago by Davide Chicco90
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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 9 days ago by Davide Chicco90
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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 11 days ago by Davide Chicco90
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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 4 months ago by Davide Chicco90
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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 4 months ago by Davide Chicco90
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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 4 months ago by Davide Chicco90 • updated 4 months ago by h.mon27k
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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 4 months ago by Davide Chicco90
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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 6 months ago by Davide Chicco90
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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 6 months ago by Davide Chicco90 • updated 6 months ago by Pierre Lindenbaum123k
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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 7 months ago by Davide Chicco90

Latest awards to Davide Chicco

Appreciated 4 months ago, created a post with more than 5 votes. For Affymetrix Gene Id Format - What Does "At" Stand For?
Great Question 4 months ago, created a question with more than 5,000 views. For Affymetrix Gene Id Format - What Does "At" Stand For?
Popular Question 4.9 years ago, created a question with more than 1,000 views. For Affymetrix Gene Id Format - What Does "At" Stand For?
Popular Question 7.8 years ago, created a question with more than 1,000 views. For Affymetrix Gene Id Format - What Does "At" Stand For?
Student 7.8 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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