User: chris86

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chris86 • 320
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UCL, United Kingdom
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I am a post-doc data analyst working in Rhuematoid Arthritis research in London.

Posts by chris86

<prev • 133 results • page 1 of 14 • next >
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Answer: A: Choosing genes for clustering
... This is common. There are ways of calculating cluster strength and stability which you could apply to different numbers of DE genes, however, this is a danger of being a bit too selective here. I would just test a few different numbers, 30, 50, 100, etc. Then choose what you need, it depends on what ...
written 10 days ago by chris86 • 320
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Answer: A: Bayesian Network analysis of gene regulatory relationship
... As far as I understand it, bayesian networks are just an alternative to correlation networks (WGCNA) or mutual information networks (ARACNE). I think your false positive rate would probably be high, but it is a valid way of finding candidates, whether it is methodologically sound.... I think that is ...
written 12 days ago by chris86 • 320
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Comment: C: Some doubts about the limma package
... No the primary research papers are what you need to read buddy. ...
written 4 weeks ago by chris86 • 320
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Comment: C: Some doubts about the limma package
... You need to read the limma papers, just search for 'limma linear models' in google scholar or anything like that. Limma uses normalised data, like quantile normalised, you should be able to normalise within the package. ...
written 4 weeks ago by chris86 • 320
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Answer: A: When is centering and scaling needed before doing hierarchical clustering?
... Scaling is only necessary when you are combining data of different types, like height and weight for example. Centering is done in principal component analysis for instance, it is not needed for clustering as it will not effect the results. You could also consider trying kmeans with the silhouette ...
written 5 weeks ago by chris86 • 320
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Tximport with paired and single ended reads
... Hi I am currently running tximport on my RNA-seq salmon count data, unfortunately we have a batch that is single ended reads. Is it appropriate to read all samples in together and then export the normalized counts etc for downstream analysis, or should I do this separately for single and paired rea ...
limma bioconductor rna-seq written 5 weeks ago by chris86 • 320
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Paired t-test with 2 groups, how to I tell the DEGs between them?
... Hi I have 2 groups in my cohort those who respond to a drug and those who do not, I am looking at what changes between them between 2 timepoints. I have currently done a paired t-test on both groups separately to get the DEGs for each group. However, if I want to know which DEGs are different signi ...
limma written 8 weeks ago by chris86 • 320 • updated 8 weeks ago by James W. MacDonald ♦ 44k
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Comment: C: Batch effect between paired and single ended reads
... OK thanks again Gordon. ...
written 10 weeks ago by chris86 • 320
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Batch effect between paired and single ended reads
... Hi We have one batch which was done with single ended illumina reads and the rest paired. I ran salmon paired end mode for the other batches then changed to single ended mode for the singled ended reads. I then imported all the data together using tximport. I then did VST using DESEQ2 and did a PCA ...
rnaseq written 10 weeks ago by chris86 • 320 • updated 10 weeks ago by Gordon Smyth ♦ 31k
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Answer: A: Which raw files (RNAseq) to download?
... The files you are looking for are here: http://www.ebi.ac.uk/ena/data/view/PRJEB14614 You can start with the .fastq files from the FTP. ...
written 3 months ago by chris86 • 320

Latest awards to chris86

Popular Question 3 months ago, created a question with more than 1,000 views. For Limma camera function never gives any differentially expressed gene sets
Autobiographer 16 months ago, has more than 80 characters in the information field of the user's profile.
Supporter 17 months ago, voted at least 25 times.
Scholar 17 months ago, created an answer that has been accepted. For A: Apply the plotPCA function in DESeq2 package to quantitative MS-based data
Centurion 17 months ago, created 100 posts.
Scholar 17 months ago, created an answer that has been accepted. For A: Heatmap of a subset of genes
Student 17 months ago, asked a question with at least 3 up-votes. For Limma camera function never gives any differentially expressed gene sets
Scholar 17 months ago, created an answer that has been accepted. For A: Heatmap of a subset of genes
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