User: Stane

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Stane40
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9 months, 3 weeks ago
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2 years, 4 months ago
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Posts by Stane

<prev • 24 results • page 1 of 3 • next >
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Comment: C: Inconsistency of results GSEA clusterprofiler
... I just bumped the nPerm to 5k and now the results seems more consistent ...
written 10 months ago by Stane40
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Inconsistency of results GSEA clusterprofiler
... Hello,  I have been trying to reproduce results from gsea using clusterprofiler and gseKEGG (for some unknow reason gseGO is not working for me ) simply repeating experiment on the same gene expression data about 13k genes:   gseKEGG(geneList = zscores,                       organism = 'hsa',   ...
clusterprofiler gsea written 10 months ago by Stane40
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Retrieving all genes related a go term
... Hello,  I am trying to improve the way that I am retrieving genes related to a go term, getting something closer to amigo/quickgo (are they the most up to date ?) I have two simple ways so far:  AnnotationDbi::select(org.Hs.eg.db, keys=go_key, ...
go biomart annotationdbi R written 14 months ago by Stane40 • updated 14 months ago by James W. MacDonald48k
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Annotation dbi error GO term
... Hi I am getting this error with the following code, the go key  AnnotationDbi::select(org.Hs.eg.db, keys='GO:1990281',                         columns = c("SYMBOL"),                         keytype = "GOALL")   error message :  None of the keys entered are valid keys for 'GOALL' my guess is thi ...
go annotationdbi written 14 months ago by Stane40 • updated 14 months ago by James W. MacDonald48k
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Comment: C: drawing chemical from smile 2D/3D
... Thank you Thomas for your help the recommendation about Avogadro ! ...
written 16 months ago by Stane40
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drawing chemical from smile 2D/3D
... Hello, I have been drawing chemical from smile using python package rdkit and I was wondering if it could be possible to do the same from R as I am using R much more in my work. I played with ChemmineR which seems great but I can't figure out how to make it work fully. first if I try converting my ...
chemminer written 17 months ago by Stane40 • updated 17 months ago by Thomas Girke1.7k
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Comment: C: Design question limma multi variables
... Thank you so much for your explanation you really are a great help. I understood the second part concerning the contrast, it is additional coefficients that lmFit apply to the related column off the design. And the following contrast which I find more clear:  con <- makeContrasts((A1 + B1 + C2 ...
written 21 months ago by Stane40
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Comment: C: Design question limma multi variables
... Thank you so much Aaron, I am starting to understand :) concerning the toy example additive model, do you say that the cell_classTrue is the effect of treatment2 over control only as the row with 1 exactly match the row with 1 in treatment2 and not treatment1 ? in my additive design with all the dat ...
written 21 months ago by Stane40
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Comment: C: Design question limma multi variables
... Thank you for taking the time Aaron, you resumed pretty well the situation in your code, I just simplified and I changed it a little to reflect the fact that I have a least 2 control per cell line, some cell lines are more represented than others and a few cell line have more than one treatment meth ...
written 21 months ago by Stane40
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Comment: C: Design question limma multi variables
... Thanks but I wouldn't ask if it was that simple, well I am not interested in the slight difference between treatments, my interest is in the general picture of the cell control vs treated(any treatment method) Let suppose I didn't mention the treatment_methods and only add the cell_lines informatio ...
written 21 months ago by Stane40

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