User: chris86
chris86 • 380
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I am a post-doc data analyst working in Rhuematoid Arthritis research in London.
Posts by chris86
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... 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
chris86 • 380
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... 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
chris86 • 380
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... 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
chris86 • 380
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... 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
chris86 • 380
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... 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
chris86 • 380
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... 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 ...
written 9 weeks ago by
chris86 • 380
• updated
9 weeks ago by
Gordon Smyth ♦ 38k
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... 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
chris86 • 380
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... 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
chris86 • 380
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... 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
chris86 • 380
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... 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
chris86 • 380
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