User: Lluís R

gravatar for Lluís R
Lluís R300
Reputation:
300
Status:
Trusted
Location:
European Union
Last seen:
16 hours ago
Joined:
2 years, 10 months ago
Email:
l************@gmail.com

I am the author and maintainer of the BioCor package

Posts by Lluís R

<prev • 161 results • page 2 of 17 • next >
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Comment: C: installing xcms and faahKO package
... The problem seems to come from here: > unable to update packages: boot, Matrix, mgcv You should install it as an admin of your computer to have rights to install/update that packages. Also that might be the reason why you can't install faahKO ...
written 7 weeks ago by Lluís R300 • updated 7 weeks ago by Martin Morgan ♦♦ 20k
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Answer: A: WGCNA TOMType specification
... TOMType options handles how should conflicting TOMs be handled (TOM between gene A and B is +, between A and C is +, and between B and C is -), usually there are few conflicts that's why it doesn't make much of a difference. The NetworkType option is described in the adjacency function. There it say ...
written 7 weeks ago by Lluís R300
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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 8 weeks ago by Lluís R300
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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 8 weeks ago by Lluís R300
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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 8 weeks ago by Lluís R300
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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 8 weeks ago by Lluís R300
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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 9 weeks ago by Lluís R300
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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 10 weeks ago by Lluís R300
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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 10 weeks ago by Lluís R300
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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 10 weeks ago by Lluís R300

Latest awards to Lluís R

Scholar 4 months ago, created an answer that has been accepted. For A: WGCNA: What is `soft thresholding`?
Teacher 4 months 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 5 months ago, voted more than 100 times.
Centurion 7 months ago, created 100 posts.
Scholar 2.8 years ago, created an answer that has been accepted. For A: WGCNA: What is `soft thresholding`?
Supporter 2.8 years ago, voted at least 25 times.

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