User: chris86

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chris86380
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UCL, United Kingdom
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https://intobioinforma...
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1 week, 5 days ago
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3 years, 9 months ago
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I am a post-doc data analyst working in Rhuematoid Arthritis research in London.

Posts by chris86

<prev • 171 results • page 1 of 18 • next >
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Comment: C: Error in reading data on isoformswitchanalyzeR
... Try doing some example read alignments and then just trying to input the directory into R. I am having no problems with it, I'm using the latest version of salmon and not changing the output folder files and structure at all afterwards. ...
written 20 days ago by chris86380
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Comment: C: Error in reading data on isoformswitchanalyzeR
... If you are sure your output directories are as normal (they match example ones), then ask here for more help, https://github.com/kvittingseerup/IsoformSwitchAnalyzeR/issues. ...
written 20 days ago by chris86380
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Comment: C: Error in reading data on isoformswitchanalyzeR
... OK, I think there is something different with your salmon output directories. I don't know what that is. Make sure your output directories contain all the files and folders normally outputted by salmon into a directory per sample. ...
written 20 days ago by chris86380
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Comment: C: Error in reading data on isoformswitchanalyzeR
... Can you work through the example data successfully first? https://bioconductor.org/packages/release/bioc/vignettes/IsoformSwitchAnalyzeR/inst/doc/IsoformSwitchAnalyzeR.html I suggest reading the section in the longer workflow called ' Importing Data from Kallisto, Salmon, RSEM or StringTie'. It is ...
written 20 days ago by chris86380
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Comment: C: Transcript variant analysis on Salmon output
... Yeah you don't need the BAM file anymore, you can just use the salmon counts with isoswitchanalyser. If you want new gene models you can generate them using hisat2 and stringtie or strawberry, this is a lot more work and a different pipeline. People do this if they think their annotation is not tha ...
written 22 days ago by chris86380
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Comment: C: Transcript variant analysis on Salmon output
... If you mean isoform level transcript DE analysis you can use Sleuth (https://github.com/pachterlab/sleuth), accessible through the wasabi package (https://github.com/COMBINE-lab/wasabi). If you mean splicing analysis, it is better to use isoswitchanalyser in my opinion (https://bioconductor.org/pack ...
written 22 days ago by chris86380
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Answer: A: Consensus Cluster Plus pre-computed distance matrix
... May be better to pre-filter your data-set features based on the co efficient of variation. Your unlikely to need 50,000 features. I also find the delta K with that method subjective to what constitutes the best number of clusters and it can't handle higher numbers of clusters. An alternative to thi ...
written 27 days ago by chris86380
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Comment: C: DEXSeq With Reduced Annotations
... Can't see why that would matter unless you have pre-selected those genes due to a prior statistical test and therefore would be biasing your results. ...
written 5 weeks ago by chris86380
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Highly uneven mapping rates and counts between samples
... Hi I have Illumina mRNA-seq samples where it seems because of low RINs (2-4) in a bunch of them compared to the others, I am getting very widely varying mapping rates (15%-70%) and therefore counts per sample (e.g. 8,000,000 mapped reads vs 40,000,000). Plus I can't really use RIN/mapping rate as a ...
normalization limma deseq2 written 11 weeks ago by chris86380 • updated 11 weeks ago by Aaron Lun23k
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Answer: A: feature reduction using machine learning
... Your question is not specific enough. Machine learning can mean a great number of things. ...
written 4 months ago by chris86380

Latest awards to chris86

Popular Question 4 months ago, created a question with more than 1,000 views. For Prior plots from COMBAT
Popular Question 10 months ago, created a question with more than 1,000 views. For Limma camera function never gives any differentially expressed gene sets
Popular Question 10 months ago, created a question with more than 1,000 views. For Limma un moderated t-test
Scholar 22 months ago, created an answer that has been accepted. For A: Heatmap of a subset of genes
Popular Question 22 months ago, created a question with more than 1,000 views. For Variance filtering prior to RNA-seq differential expression
Popular Question 22 months ago, created a question with more than 1,000 views. For Limma camera function never gives any differentially expressed gene sets
Popular Question 22 months ago, created a question with more than 1,000 views. For Prior plots from COMBAT
Popular Question 22 months ago, created a question with more than 1,000 views. For Limma camera function never gives any differentially expressed gene sets
Autobiographer 3.0 years ago, has more than 80 characters in the information field of the user's profile.
Centurion 3.0 years ago, created 100 posts.
Scholar 3.0 years ago, created an answer that has been accepted. For A: Heatmap of a subset of genes
Student 3.0 years ago, asked a question with at least 3 up-votes. For Limma camera function never gives any differentially expressed gene sets
Scholar 3.0 years ago, created an answer that has been accepted. For A: Apply the plotPCA function in DESeq2 package to quantitative MS-based data
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Scholar 3.0 years ago, created an answer that has been accepted. For A: Heatmap of a subset of genes

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