User: Lluís R

gravatar for Lluís R
Lluís R210
Reputation:
210
Status:
Trusted
Location:
European Union
Last seen:
10 hours ago
Joined:
2 years, 5 months ago
Email:
l************@gmail.com

I am the author and maintainer of the BioCor package

Posts by Lluís R

<prev • 127 results • page 1 of 13 • next >
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Comment: C: limma: same data in different formats produces different DEG-analysis results
... You need to fit the linear model with all the samples and then use the contrasts to compare the genes for that tissue between those phenotypes. This may require to tweak your design table. ...
written 15 hours ago by Lluís R210
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Comment: C: R package help
... I am sure you read https://github.com/Bioconductor/Contributions#what-to-expect. Please be patient, until your packages builds correctly (without a warning or an error of your package) it won't be reviewed. On a technical note, there are some code in the test files which are not tests. ...
written 18 hours ago by Lluís R210
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Comment: C: Getting Differentially Expressed Genes from GOSeq Categories
... How do you decide if a gene is differentially expressed in diff_exp_ensembl ? The reason of dissagrement might be that a gene is considered DE differently in GOSeq and by your vector (If I understood correctly the question). ...
written 1 day ago by Lluís R210
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Comment: C: Pathview error: ran fine yesterday
... Could you please show us the code that produced this error?  Which version of Pathview do you use ? ...
written 3 days ago by Lluís R210
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Comment: C: limma: same data in different formats produces different DEG-analysis results
... How did you evaluate the comparison between cell7 and cell8 in the first analysis? Did you use constrasts? How have you corrected the batch effect in the second analysis and in the first? ...
written 3 days ago by Lluís R210
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Answer: A: how to use q value to select differentially expressed genes
... The threshold for considering a fold change significant is arbitrary (but usually the q-value below 0.05 is used) ...
written 3 days ago by Lluís R210
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Comment: C: signed kME(MM) for finding hub genes in modules of interest
... Why did you not restrict the selection of hub genes to the subset of genes assigned to the brown module? You are interested in hub genes of that module, aren't you? So don't subset all the genes, As you can see in the linked question I personally don't like to select hub genes by the absolute value ...
written 6 days ago by Lluís R210
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Testing a gene set with globaltest
... I am trying to use the function gtBroad with my own custom gene set collection created with GSEABase and an expression set but gtBroad is still asking for annotation. But when given it cannot annotate (because it is already there I think): > gs GeneSetCollection names: KEGG_GLYCOLYSIS_GLUCONE ...
globaltest written 8 days ago by Lluís R210
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Comment: C: WGCNA: error message in blockwiseModule(): address 0x0, cause 'memory not mapped
... This seems to be a bug, in the C code. Were you going through the tutorial? ...
written 11 days ago by Lluís R210
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Comment: C: PhD student positions in the areas of Bioinformatics, Computer Science and Biost
... What has changed from your call in October (October) and January (January)? I see the same description each time. Is the project the same? ...
written 23 days ago by Lluís R210

Latest awards to Lluís R

Voter 22 days ago, voted more than 100 times.
Centurion 12 weeks ago, created 100 posts.
Scholar 2.4 years ago, created an answer that has been accepted. For A: WGCNA: What is `soft thresholding`?
Supporter 2.4 years ago, voted at least 25 times.

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