User: chris86

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chris86380
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380
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UCL, United Kingdom
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https://intobioinforma...
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6 hours ago
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3 years, 11 months ago
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I am a post-doc data analyst working in Rhuematoid Arthritis research in London.

Posts by chris86

<prev • 174 results • page 1 of 18 • next >
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Comment: C: Limma classical interaction model question
... OK Gordon, I actually have already done as you suggest in the manual and used the single factor method by pasting the groups together. So your saying the above when you test response*drug is not the same interaction as I would be testing by using (responderDrug1-non-responderDrug1)-(responderDrug2-n ...
written 9 hours ago by chris86380
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Comment: C: Limma classical interaction model question
... OK thanks Gordon, so how would I modify the second block of code to test the same hypothesis as the first? ...
written 10 hours ago by chris86380
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Limma classical interaction model question
... Hi So I am trying to work out why these two bits of code give different results. The overall aim is to look for genes that are changing differently between responders and non-responders (to therapy) between two different treatment groups (baseline only data i.e. a single timepoint). However, I am a ...
limma written 12 hours ago by chris86380 • updated 11 hours ago by Gordon Smyth37k
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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 10 weeks 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 10 weeks 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 10 weeks 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 10 weeks 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 11 weeks 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 11 weeks 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 11 weeks ago by chris86380

Latest awards to chris86

Popular Question 6 months ago, created a question with more than 1,000 views. For Prior plots from COMBAT
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 Limma un moderated t-test
Scholar 24 months ago, created an answer that has been accepted. For A: Heatmap of a subset of genes
Popular Question 24 months ago, created a question with more than 1,000 views. For Variance filtering prior to RNA-seq differential expression
Popular Question 24 months ago, created a question with more than 1,000 views. For Limma camera function never gives any differentially expressed gene sets
Popular Question 24 months ago, created a question with more than 1,000 views. For Prior plots from COMBAT
Popular Question 2.0 years ago, created a question with more than 1,000 views. For Limma camera function never gives any differentially expressed gene sets
Autobiographer 3.1 years ago, has more than 80 characters in the information field of the user's profile.
Centurion 3.1 years ago, created 100 posts.
Scholar 3.1 years ago, created an answer that has been accepted. For A: Heatmap of a subset of genes
Student 3.1 years ago, asked a question with at least 3 up-votes. For Limma camera function never gives any differentially expressed gene sets
Scholar 3.1 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 3.2 years ago, created an answer that has been accepted. For A: Heatmap of a subset of genes

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