User: Agustin Gonzalez-Vicente

Reputation:
40
Status:
New User
Location:
Cleveland, OH
Twitter:
@AgustinGonVi
Last seen:
1 month, 2 weeks ago
Joined:
6 months, 1 week 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 9 weeks ago by Agustin Gonzalez-Vicente40
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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 10 weeks ago by Agustin Gonzalez-Vicente40
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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 10 weeks ago by Agustin Gonzalez-Vicente40
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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 10 weeks ago by Agustin Gonzalez-Vicente40 • updated 9 weeks ago by zx87547.9k
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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 10 weeks ago by Agustin Gonzalez-Vicente40
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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 10 weeks ago by Agustin Gonzalez-Vicente40
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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 10 weeks ago by Agustin Gonzalez-Vicente40
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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 6 months ago by Agustin Gonzalez-Vicente40

Latest awards to Agustin Gonzalez-Vicente

Autobiographer 9 weeks ago, has more than 80 characters in the information field of the user's profile.
Scholar 10 weeks ago, created an answer that has been accepted. For A: WGCNA: Relating Eigenmodules to Clinical Traits Returns Matrix of NAs
Scholar 10 weeks ago, created an answer that has been accepted. For A: WGCNA: Relating Eigenmodules to Clinical Traits Returns Matrix of NAs

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