User: swbarnes2

gravatar for swbarnes2
swbarnes2240
Reputation:
240
Status:
Trusted
Location:
Last seen:
12 hours ago
Joined:
1 year, 10 months ago
Email:
s********@gmail.com

Posts by swbarnes2

<prev • 76 results • page 1 of 8 • next >
0
votes
2
answers
80
views
2
answers
Comment: C: Two controls in RNAseq formula for DESeq2
... Okay, so you observed this: > The key point to remember about designs with interaction terms is > that, unlike for a design ~genotype + condition, where the condition > effect represents the overall effect controlling for differences due > to genotype, by adding genotype:condition, the ...
written 6 days ago by swbarnes2240
0
votes
2
answers
80
views
2
answers
Comment: C: Two controls in RNAseq formula for DESeq2
... Sorry, I misspoke in my answer. But your question is incomplete without saying exactly what comparison you are asking for in results, because the default is going to be to give you the genes which respond differently to treatment between sex, and it's not at all clear to me that that's what you rea ...
written 6 days ago by swbarnes2240
0
votes
2
answers
80
views
2
answers
Answer: A: Two controls in RNAseq formula for DESeq2
... Use contrasts to specify what condition should be compared to what. Running DESeq without specifying the contrasts is dangerous, you might not be doing the contrast you think you are. Especially with that design; I'm pretty sure you are not doing the contrast you intend. ...
written 6 days ago by swbarnes2240
0
votes
1
answer
95
views
1
answers
Comment: C: understanding DEseq2 interactions before/after releveling the baseline
... Just make it easier for people to help you. Write out explicitly how everything is leveled at each step, every design command line, and every results call. ...
written 13 days ago by swbarnes2240
1
vote
2
answers
89
views
2
answers
Answer: A: deseq2 formula design
... If each village is in exactly one region, you can't put village and region in the design. Pick one or the other. ...
written 24 days ago by swbarnes2240
0
votes
1
answer
140
views
1
answers
Comment: C: Questions for ResultsNames() and the Contrast function
... You need to add what the design is for your examples, as adding the interaction term changes the meaning of some of the examples. I strongly recommend making a dummy data set as the second link shows, getting the normalized counts, and confirming in Excel what all the different kinds of contrasts d ...
written 26 days ago by swbarnes2240
1
vote
1
answer
109
views
1
answers
Answer: A: Importance of Order in Design Formula
... https://rdrr.io/bioc/DESeq2/man/results.html > If results is run without specifying contrast or name, it will return > the comparison of the last level of the last variable in the design > formula over the first level of this variable. If you specify the contrast you want, order doesn't m ...
written 26 days ago by swbarnes2240
0
votes
1
answer
101
views
1
answers
Answer: A: deseq2 correction batch effect without design
... DESeq does not correct the batch effect, it incorporates it into its linear model making. And you do that just like above, by adding batch to the design along with the other elements of the experiment. ...
written 28 days ago by swbarnes2240
0
votes
2
answers
83
views
2
answers
Answer: A: DESeq2 "Not full rank" Error
... That design will likely not work, and is likely not what you want anyway. (Species is confounded with sex, because you didn't get all the same sexes for all the species, so you can't do that interaction) To contrast a subset of samples against a subset of samples, make a new column like the vignet ...
written 4 weeks ago by swbarnes2240
0
votes
1
answer
115
views
1
answers
Answer: C: RNA-seq time course analysis with only one experimental condition
... If all the samples have the same condition value, it shouldn't be in the design. ...
written 4 weeks ago by swbarnes2240

Latest awards to swbarnes2

Scholar 24 days ago, created an answer that has been accepted. For C: Principal components in DESeq2
Scholar 4 weeks ago, created an answer that has been accepted. For C: Principal components in DESeq2
Supporter 4 weeks ago, voted at least 25 times.
Scholar 8 months ago, created an answer that has been accepted. For C: Principal components in DESeq2
Teacher 8 months ago, created an answer with at least 3 up-votes. For A: Appropriate experimental design for differential expresion

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 16.09
Traffic: 330 users visited in the last hour