User: Agustin Gonzalez-Vicente

Reputation:
60
Status:
New User
Location:
Cleveland, OH
Twitter:
@AgustinGonVi
Last seen:
8 months, 3 weeks ago
Joined:
1 year, 3 months ago
Email:
a************@gmail.com

I’m a renal physiologist focused on genomics and data analysis. I work in association with a research group conducting both basic and clinical research. My goal is to use bioinformatics tools to answer biological questions relevant to renal disease mechanisms.

I primarily use R in R-Studio which I complement with desktop and web-based resources, mostly Galaxy, Ensembl, Cytoscape, Ingenuity Pathway Analysis (Qiagen) and WikiPathways.

Posts by Agustin Gonzalez-Vicente

<prev • 8 results • page 1 of 1 • next >
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Comment: A: WGCNA: error in numbers2color
... In looks like the column "comments" its not numeric, eliminate that one and try it again. Also look at the help("numbers2colors"). ...
written 11 months ago by Agustin Gonzalez-Vicente60
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Answer: A: WGCNA categorical trait with more than 2 levels.
... You can use categorical variables, if it is binary, then you can expressed it as 0 and 1. If it has more levels then you can separate each level as an individual binary variable. [This link may help][1] [1]: https://peterlangfelder.com/2018/11/25/working-with-categorical-variables/ ...
written 11 months ago by Agustin Gonzalez-Vicente60
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Answer: A: Threshold of removing genes with low counts ?
... This may be of some interest. [Filtering and collapsing data][1] [1]: https://peterlangfelder.com/2018/11/25/filtering-and-collapsing-data/ ...
written 11 months ago by Agustin Gonzalez-Vicente60
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Strong covariates and weak biological signal in transcriptomes
... My experiment aims to test the interaction between heterologous genes in a double transgenic mouse model. Basically the interaction of viral genes with 3 different variants of a human gene. The gene expression data was obtained with Affymetrix microarrays, and present 2 unwanted (and strong) sources ...
R sva written 11 months ago by Agustin Gonzalez-Vicente60 • updated 11 months ago by zx87549.2k
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Comment: C: RNASeq alignment and quantification for a transgenic mouse
... Thanks, do you know of any detailed tutorial to do that? I am working with RNAseq from GEO, there is no info about the location of the insertion. ...
written 11 months ago by Agustin Gonzalez-Vicente60
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Answer: A: WGCNA: Relating Eigenmodules to Clinical Traits Returns Matrix of NAs
... You have to express categorical variables as dichotomous numeric. For example creating a variable named 1stBatch and assign 1 to all samples on 1st batch and 0 to the rest. and repeat this process with all variables of interest ...
written 11 months ago by Agustin Gonzalez-Vicente60
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Comment: C: RNASeq alignment and quantification for a transgenic mouse
... I have a similar issue to that presented above with the exception that no gene was replaced. Instead a human gene with no-mouse ortholog together with GFP under the same promoter. How do I append and new chromosome to the genome to quantify expression? Thanks! ...
written 11 months ago by Agustin Gonzalez-Vicente60
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Comment: A: removing batch effects using ComBat and SVA
... Hi, I cannot download the bladderdata example and I am having problems with the format of the matrices to run ComBat. How dat, batch and mod should be formatted? Thanks. ...
written 15 months ago by Agustin Gonzalez-Vicente60

Latest awards to Agustin Gonzalez-Vicente

Autobiographer 11 months ago, has more than 80 characters in the information field of the user's profile.
Scholar 11 months ago, created an answer that has been accepted. For A: WGCNA: Relating Eigenmodules to Clinical Traits Returns Matrix of NAs
Scholar 11 months ago, created an answer that has been accepted. For A: WGCNA: Relating Eigenmodules to Clinical Traits Returns Matrix of NAs

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