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

Posts by chris86

<prev • 177 results • page 1 of 18 • next >
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Comment: C: How to apply a linear mixed model onto an RNA-Seq data?
... Correct me if I’m wrong, but I think the duplicatecorrelation function in limma is equivalent to adding a random effect. ...
written 6 days ago by chris86380
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Comment: C: Variance stabilising transformation for machine learning
... Indeed I use the vst function all the time before running caret or clustering etc, it is very useful, you misunderstood my point. There isn’t a lot of good sense to using deseq2 to select features to make a classification model to me, seeing as many algorithms will select features for you according ...
written 6 days ago by chris86380
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Comment: C: Variance stabilising transformation for machine learning
... It’s an unusual idea to pre select genes ranked according to a prior statistical test. If you read the caret manual they suggest allowing the underlying algorithm to select features automatically eg glmnet. There is also the overfitting issue if you haven’t cross validated the feature selection with ...
written 6 days ago by chris86380
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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 weeks 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 9 weeks 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 9 weeks ago by chris86380 • updated 9 weeks ago by Gordon Smyth38k
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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 4 months 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 4 months 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 4 months 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 4 months ago by chris86380

Latest awards to chris86

Popular Question 8 months ago, created a question with more than 1,000 views. For Prior plots from COMBAT
Popular Question 14 months ago, created a question with more than 1,000 views. For Limma camera function never gives any differentially expressed gene sets
Popular Question 14 months ago, created a question with more than 1,000 views. For Limma un moderated t-test
Scholar 2.2 years ago, created an answer that has been accepted. For A: Heatmap of a subset of genes
Popular Question 2.2 years ago, created a question with more than 1,000 views. For Variance filtering prior to RNA-seq differential expression
Popular Question 2.2 years ago, created a question with more than 1,000 views. For Limma camera function never gives any differentially expressed gene sets
Popular Question 2.2 years ago, created a question with more than 1,000 views. For Prior plots from COMBAT
Popular Question 2.2 years ago, created a question with more than 1,000 views. For Limma camera function never gives any differentially expressed gene sets
Autobiographer 3.3 years ago, has more than 80 characters in the information field of the user's profile.
Centurion 3.3 years ago, created 100 posts.
Scholar 3.3 years ago, created an answer that has been accepted. For A: Heatmap of a subset of genes
Student 3.3 years ago, asked a question with at least 3 up-votes. For Limma camera function never gives any differentially expressed gene sets
Scholar 3.3 years ago, created an answer that has been accepted. For A: Apply the plotPCA function in DESeq2 package to quantitative MS-based data
Supporter 3.3 years ago, voted at least 25 times.
Scholar 3.3 years ago, created an answer that has been accepted. For A: Heatmap of a subset of genes

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