User: chris86

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chris86380
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380
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Trusted
Location:
UCL, United Kingdom
Last seen:
2 hours ago
Joined:
2 years, 11 months ago
Email:
c*************@gmail.com

I am a post-doc data analyst working in Rhuematoid Arthritis research in London.

Posts by chris86

<prev • 154 results • page 1 of 16 • next >
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ANOVA in ROAST
... Hi I want to implement an ANOVA in ROAST from the limma package? Is this possible? The last thread I found was 4 years old and said it was yet to be included in the package.... I think this would be very useful, I am a big fan of ROAST. Best wishes, Chris ...
limma written 2 days ago by chris86380 • updated 2 days ago by Gordon Smyth33k
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Comment: C: Better to use rlog or vst transformation for data quality assessment of differen
... If it helps, I don't think there is usually much difference between the two. I use VST because it is a lot faster... personally. ...
written 14 days ago by chris86380
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Comment: C: novice: building gene co-expression network using RNA-Seq data
... It's all in the WGCNA manual I believe, what you are doing. ...
written 9 weeks ago by chris86380
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Comment: C: Update from developers branch of bioconductor packages
... Thanks Mike. ...
written 9 weeks ago by chris86380
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Update from developers branch of bioconductor packages
... Hi I am just wondering when my package will be updated (M3C) from the development branch which has been more developed than the stable release for a number of months now. There are no build errors atm. Best wishes, Chris ...
bioconductor written 9 weeks ago by chris86380 • updated 9 weeks ago by Mike Smith2.7k
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Comment: C: Clustering of samples based on specific gene sets
... You could just aggregate the gene set genes by their mean, if that makes sense... Then you would be clustering gene sets instead of genes. ...
written 3 months ago by chris86380
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Comment: C: Clustering of samples based on specific gene sets
... Hi, sorry, but this isn't much of a question as you have the answer there already.. you would cluster samples using just the gene sets your interested in. Which typically means sub-setting the rows just to contain the genes that are the members of the gene sets you are interested in. ...
written 3 months ago by chris86380
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Answer: A: Is there any prerequisites for taking correlation in genomic data?
... When is expression not meaningful? We typically filter genes based on an abundance threshold before doing analyses (e.g. a CPM cut off), is this what you mean? Should you exclude samples based on z-score? I wouldn't remove samples unless they are clear outliers based on a global gene expression p ...
written 3 months ago by chris86380
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CAMERA fold changes per gene set?
... Dear bioconductor/ limma developers I was wondering if there is a straightforward way of getting fold changes per gene set out when I run CAMERA or any of the gene set functions in limma. This is because I need to plot them. I am enjoying using the general pipeline, but at the moment to get the fol ...
limma written 5 months ago by chris86380
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Comment: C: Paired factorial design model in limma
... Thanks Aaron ...
written 6 months ago by chris86380

Latest awards to chris86

Popular Question 12 months ago, created a question with more than 1,000 views. For Variance filtering prior to RNA-seq differential expression
Popular Question 12 months ago, created a question with more than 1,000 views. For Limma camera function never gives any differentially expressed gene sets
Popular Question 12 months ago, created a question with more than 1,000 views. For Prior plots from COMBAT
Scholar 12 months ago, created an answer that has been accepted. For A: Heatmap of a subset of genes
Popular Question 12 months ago, created a question with more than 1,000 views. For Limma camera function never gives any differentially expressed gene sets
Autobiographer 2.1 years ago, has more than 80 characters in the information field of the user's profile.
Centurion 2.2 years ago, created 100 posts.
Scholar 2.2 years ago, created an answer that has been accepted. For A: Heatmap of a subset of genes
Scholar 2.2 years ago, created an answer that has been accepted. For A: Apply the plotPCA function in DESeq2 package to quantitative MS-based data
Supporter 2.2 years ago, voted at least 25 times.
Student 2.2 years ago, asked a question with at least 3 up-votes. For Limma camera function never gives any differentially expressed gene sets
Scholar 2.2 years ago, created an answer that has been accepted. For A: Heatmap of a subset of genes

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