User: Lluís R

gravatar for Lluís R
Lluís R270
Reputation:
270
Status:
Trusted
Location:
European Union
Last seen:
1 day, 13 hours ago
Joined:
2 years, 8 months ago
Email:
l************@gmail.com

I am the author and maintainer of the BioCor package

Posts by Lluís R

<prev • 149 results • page 1 of 15 • next >
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Comment: C: RNseq data for WGCNA
... I think you can add a limit on your module size, or given the TOM distance you could build different networks by cutting at different heights. Maybe there isn't correlation between the group and the traits you are testing. You could also check if building other type of networks adjacency(..., type = ...
written 2 days ago by Lluís R270
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Comment: C: RNseq data for WGCNA
... I don't find the problem. What do you want to improve? You would like to have more modules? ...
written 3 days ago by Lluís R270
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Comment: C: topGO - missing value where TRUE/FALSE needed
... When reading the file with read.delim, check that the quote argument has the ". Also split the second column by comma. strsplit(",", x) where x would be each row in V14. ...
written 3 days ago by Lluís R270
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Comment: C: topGO - missing value where TRUE/FALSE needed
... Your "geneID2GO" doesn't look well, it has double quotes, have you tried removing one pair of quotes from the characters? This way the `"sp0000017"` will become "sp0000017" and thus will be mapped with the geneList.   Also the GOs:"\"GO:0004672" "GO:0005524" "GO:0006468\"", should be splited by sp ...
written 4 days ago by Lluís R270
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Answer: A: Meta-analysis with WGCNA
... If you can use the most homogeneous samples for WGCNA in order to find the accurate relationship between genes (specially if you have more than 12 samples in that group Day7). If you are doing meta-analysis check the bias before proceeding any further. Check using PCA or similar techniques if the s ...
written 11 days ago by Lluís R270
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Comment: C: How to use topGO and KEGG with de-novo species
... topGO can be used with other organism if you provide your own mapping from gene to GO, see the vignette and the documentation ...
written 16 days ago by Lluís R270
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Comment: C: Problem with WGCNA - Module-trait relationship
... What code do you use for "the third step"? Are there any NA in your input data? Did you use the "complete" observations option to calculate the correlations? ...
written 19 days ago by Lluís R270
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Answer: A: Problem with WGCNA - Module-trait relationship
... The first line calculates the correlation of each trait with the egienvalue of each module, the second line gives you the p-value of said correlations for a given number of p-values. I advise you to use a function named somehow like corAndPvalue which gives both correlations and p-values takeing int ...
written 19 days ago by Lluís R270
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Answer: A: selection of interesting genes for a KS test in TopGO
... The geneSel is the selection of genes from the universe which are the genes provided. Otherwise the topGOdata doesn't know which is the gene set of interest. ...
written 4 weeks ago by Lluís R270
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Comment: C: Unable to install any bioconductor packages
... See the warning when you source biocLite: Warning message: Bioconductor version 3.4 is too old for R version 3.4.1; see https://bioconductor.org/install/#troubleshoot-biocinstaller   You have probably updated the R version without updating the Bioconductor packages.   ...
written 5 weeks ago by Lluís R270

Latest awards to Lluís R

Scholar 12 weeks ago, created an answer that has been accepted. For A: WGCNA: What is `soft thresholding`?
Teacher 12 weeks ago, created an answer with at least 3 up-votes. For A: Does anyone need to install an R package which is used by another package as imp
Voter 3 months ago, voted more than 100 times.
Centurion 5 months ago, created 100 posts.
Scholar 2.7 years ago, created an answer that has been accepted. For A: WGCNA: What is `soft thresholding`?
Supporter 2.7 years ago, voted at least 25 times.

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