User: sbrown669
sbrown669 • 20
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- 2 years, 8 months ago
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Posts by sbrown669
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3
votes
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... I am working with RNA-seq data, and I need to correct for covariates. To do this, I want to use the Bioconductor package SVA.
I want to produce a 'corrected dataset' and then use this for further analyses - to perform pairwise Pearson correlations and generate heat maps to visualise co-expression. ...
written 10 months ago by
sbrown669 • 20
3
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1
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1.3k
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1
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... Other than Limma being designed for microarray analysis, I'm not sure I have grasped the major differences in how they compute differential expression.
Also, how does this manifest in the gene calls? Is one more stringent? ...
written 2.4 years ago by
sbrown669 • 20
• updated
2.4 years ago by
Kevin Blighe ♦ 53k
3
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2
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2.1k
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2
answers
... This is what it says on PANTHER with regards to the test:
> The expression data analysis statistics now include a Bonferroni
> correction for multiple testing. The Bonferroni correction is
> important because we are performing many statistical tests (one for
> each pathway, or each onto ...
4
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2
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3.3k
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5 follow
2
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... My aim is to create a bash loop over my fastq files that are in a directory like so:
https://ibb.co/cMvx7a
whereby, paired read files are organised in the form:
1
1
2
2
3
3
etc..
I don't know a way of dealing with these paired files within the cutadapt loop
Something along these lines is wh ...
written 2.7 years ago by
sbrown669 • 20
• updated
23 months ago by
montoya.oscar • 50
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For PANTHER gene ontology - is the bonferroni correction important?
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For What are the major differences in the computation of DE genes between deseq2 and limma?
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2.4 years ago,
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For cutadapt loop and paired-end reads
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