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6 votes
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design formula question

You can't (easily) use a single design, since clone is nested within diabetic status, so you were correct using two separate designs. Your designs are correct. If you really wanted to use a single ...
Devon Ryan's user avatar
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4 votes
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How to incorportate RIN values as covariate in the design matrix?

In the DESeq2 manual there is a section titled "How can I include a continuous covariate in the design formula?" that deals with your question. Basically the process is no different from using a ...
PPK's user avatar
  • 886
3 votes
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Deciding which samples go in which batch

I found the OSAT package which does almost what I want. However it is specific for Illumina and for a limited number of plates: "plates that hold 2, 4, 8 IlluminaBeadChip chips and have 24, 48, 96 ...
llrs's user avatar
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3 votes
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Setting Contrast for DESeq2 results

Your table is not very clear. If I understood it correctly, there are three groups of t-cells, SPtetramer+, Ly49- and Ly49+ and within it there is a MOGSP vs MOG comparison. I would set colData like ...
StupidWolf's user avatar
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3 votes
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How I deal with this kind of gene expression comparision

No. If the only difference between Tumour_batch1 and Tumour_batch2 was the library prep/sequencing run, then all this will tell you is if the particular sample of RNA taken from the tumour is ...
Ian Sudbery's user avatar
  • 3,321
3 votes

Experimental Design for Differential expreression analysis

You're really running out of degrees of freedom and the only actual replicate is a single sample from another patient, so please take the results with a huge grain of salt. You can use a design of <...
Devon Ryan's user avatar
  • 19.6k
2 votes

How do I select a proper design matrix to use in DRIMSeq?

From your question I understand that you have two treatments in two mouse strains. If you are interested in general treatment effects independet of the animal strain you would use the both variables ...
PPK's user avatar
  • 886
2 votes

Deciding which samples go in which batch

I've had to go through this pain, and found the best way to do it was to simulate the model fit to start assessing the balance of covariates. I've got two notebooks available on Github, which should ...
A_Skelton73's user avatar
1 vote

Seeking Guidance on Designing DNA Sequences with Specific Criteria

It is not difficult to simulate every 10mer DNA oligo, here is some Python code that will do that: (there is probably a more elegant way to do this) ...
Maximilian Press's user avatar

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