User: chris86
chris86 • 380
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- UCL, United Kingdom
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- 6 hours ago
- Joined:
- 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
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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 hours 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 10 hours 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 12 hours ago by
chris86 • 380
• updated
11 hours ago by
Gordon Smyth ♦ 37k
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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 10 weeks 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 10 weeks 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 10 weeks 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 10 weeks ago by
chris86 • 380
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... 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
chris86 • 380
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... 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
chris86 • 380
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... 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
chris86 • 380
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