User: Gavin Kelly

gravatar for Gavin Kelly
Gavin Kelly180
Reputation:
180
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Trusted
Location:
United Kingdom / London / Francis Crick Institute
Twitter:
gavinpaulkelly
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Last seen:
12 hours ago
Joined:
2 years, 7 months ago
Email:
g*************@gmail.com

Statistician in the Bioinformatics & Biostatistics group at the Francis Crick institute

Posts by Gavin Kelly

<prev • 53 results • page 1 of 6 • next >
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Comment: C: Inverse logFC on DESeq2 Rstudio
... In your contrast=c("condition", "CTL", "HT") you're saying that you're looking at fold changes relative to "HT" - the second element in the character vector is the numerator, and the third is the level that will be denominator (or 'be subtracted' on the log scale).  Guessing that "CTL" means control ...
written 14 days ago by Gavin Kelly180
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Comment: C: DESeq2 on 2 genotypes versus 1 control
... If, by common, you mean having an identical difference (upto noise) in both genotypes when compared to control, then you could create another variable along the lines of condition2 <- ifelse(condition=="control", "control", "common_genotype") which would 'pool' the two genotypes, but this is prob ...
written 17 days ago by Gavin Kelly180
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Comment: C: How to use subSeq with DNAStringSet and information of GroupedIRanges?
... If 'pos' is a vector telling you the location of the base you're interested in, can you achieve what you want with something along the lines of subseq(data$seq, start=pos, width=1) or, if pos is only defined for certain rows, then you may need to subset data first to be those rows with a defined pos ...
written 4 weeks ago by Gavin Kelly180
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Job: Bioinformatics Position: Francis Crick Institute, London
... We're looking for an additional person to work in our bioinformatics core facility within the Francis Crick Institute (a biomedical discovery institute dedicated to understanding the fundamental biology underlying health and disease) to support our scientists in the analysis of their data (mainly fo ...
job bioinformatics uk written 5 weeks ago by Gavin Kelly180
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Answer: A: Multiple comparisons for DE analysis with DESeq2
... Yes, I think your approach of adding a combination factor (design = ~ new_column) is a correct way to carry out the analysis.  It would be possible to achieve something similar if you had a design = ~Cell_component * Type with an interaction, but it wouldn't be as transparent as the approach you've ...
written 6 weeks ago by Gavin Kelly180
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Answer: A: How to solve out the misunstanding of fake "red" "green" on the heatmap
... I don't think it's necessarily misleading that a bright colour represents a high expression; the heatmap is representing best estimates of fold-changes, rather than significances, and most people interpret them as such.  The ability to detect common directions in expression (even if they have failed ...
written 6 weeks ago by Gavin Kelly180
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Comment: C: DESeq2 model design with unequal number of time points
... If you have a specific 'shape' of time-profile you want to investigate, then maybe using time as a continuous variable would allow you to compensate for the 'missing' timepoints.  If you kept the time term linear, then you may be able to detect genes that have differential gradient (on a log-like sc ...
written 3 months ago by Gavin Kelly180
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Comment: C: strange results from differential methylation analysis using limma
... Assuming the "data_afterpreprocessed.txt" file contains beta-values of normalised samples, in the same order as the samples in the samplesheet file, I can't see anything terribly wrong with the code. Perhaps if you do an plotMD(fit2, column=4) or volcanoplot(fit2, coef=4) you might see what's drivin ...
written 3 months ago by Gavin Kelly180
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Comment: C: DESEq2 Paired samples: Baseline Versus each Timepoint
... Minor typo that might confuse a newbie: contrast=c("Timepoint", "Day1", "Baseline") ?     ...
written 3 months ago by Gavin Kelly180
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Comment: C: LIMMA paired analysis adjusting for two continuous variables - microarray data
... Don't think there's an issue with the continuous variables being constant within the subjects - does everything work ok if you have a design with of ~bmi + age + class, with a blocking factor of id?   I suppose you could add age:class (and/or bmi:class) interaction if you're worried that a gene's a ...
written 3 months ago by Gavin Kelly180

Latest awards to Gavin Kelly

Scholar 3 months ago, created an answer that has been accepted. For A: DESeq2 3-fatcor design and different interaction terms
Teacher 3 months ago, created an answer with at least 3 up-votes. For A: extracting the genes associated with the clusters
Autobiographer 3 months ago, has more than 80 characters in the information field of the user's profile.
Scholar 19 months ago, created an answer that has been accepted. For A: DESeq2 3-fatcor design and different interaction terms

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