User: chris86

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chris86 • 290
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Location:
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 • 127 results • page 1 of 13 • next >
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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 3 days ago by chris86 • 290 • updated 3 days ago by James W. MacDonald ♦ 43k
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Comment: C: Batch effect between paired and single ended reads
... OK thanks again Gordon. ...
written 14 days ago by chris86 • 290
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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 15 days ago by chris86 • 290 • updated 15 days ago by Gordon Smyth ♦ 30k
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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 7 weeks ago by chris86 • 290
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Answer: A: gene expression data analysis and batch effect methods
... You cant remove batch effects if the data is 100% confounded. Better just to ignore the normals. ...
written 8 weeks ago by chris86 • 290
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Answer: A: Outliers - to remove or to not remove that is the question
... I remove outliers when there is something obviously amiss with that sample because something went wrong with the array or sample prep i.e. clustering gives some really weird outlier. Other than that, I leave them. ...
written 9 weeks ago by chris86 • 290
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How does it work with submitting a package to the bioconductor and doing the paper together?
... Hi I am almost finished my package and the paper is nearly done too. Which order do I submit these in? Do I wait for it to be accepted by the bioconductor then submit to journal or vice versa? Thanks, Chris ...
bioconductor written 9 weeks ago by chris86 • 290 • updated 9 weeks ago by Martin Morgan ♦♦ 20k
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Calculating probability of getting xx genes past FDR10%
... Hi I was wondering if anyone could help me with the following. Of 353 detected miRNAs 74 were statistically significant (FDR 10%), if I recall correctly at 10% FDR I should expect 3.53 significant miRNAs, but what is the probability of observing 74 at this threshold. The FDR is calculated using ben ...
limma written 4 months ago by chris86 • 290 • updated 4 months ago by Gordon Smyth ♦ 30k
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Comment: C: illumina ht-12 v4 expression beadchip
... use limma and read the manual ...
written 5 months ago by chris86 • 290
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Comment: C: Negative bionomial model (test) vs T test in EBseq or DEseq2
... Just read some papers, e.g. Anders, S. and Huber, W., 2012. Differential expression of RNA-Seq data at the gene level–the DESeq package. Heidelberg, Germany: European Molecular Biology Laboratory (EMBL). Law, C.W., Chen, Y., Shi, W. and Smyth, G.K., 2014. Voom: precision weights unlock linear mode ...
written 5 months ago by chris86 • 290

Latest awards to chris86

Popular Question 7 weeks ago, created a question with more than 1,000 views. For Limma camera function never gives any differentially expressed gene sets
Autobiographer 14 months ago, has more than 80 characters in the information field of the user's profile.
Supporter 15 months ago, voted at least 25 times.
Scholar 15 months ago, created an answer that has been accepted. For A: Apply the plotPCA function in DESeq2 package to quantitative MS-based data
Centurion 15 months ago, created 100 posts.
Scholar 15 months ago, created an answer that has been accepted. For A: Heatmap of a subset of genes
Student 15 months ago, asked a question with at least 3 up-votes. For Limma camera function never gives any differentially expressed gene sets
Scholar 15 months ago, created an answer that has been accepted. For A: Heatmap of a subset of genes
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