User: sbrown669

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sbrown66920
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1 year, 1 month ago
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3 years, 7 months ago
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Posts by sbrown669

<prev • 4 results • page 1 of 1 • next >
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Using SVA to correct for covariates in RNA-seq data
... 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. ...
R sva corrections covariates rna-seq written 22 months ago by sbrown66920
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What are the major differences in the computation of DE genes between deseq2 and limma?
... 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? ...
R deseq2 limma differential expression rna-seq written 3.4 years ago by sbrown66920 • updated 3.4 years ago by Kevin Blighe69k
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PANTHER gene ontology - is the bonferroni correction important?
... 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 ...
panther ontology rna-seq statistics written 3.4 years ago by sbrown66920 • updated 3.4 years ago by mforde841.3k
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cutadapt loop and paired-end reads
... 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 ...
paired-end cutadapt loop rna-seq bash written 3.7 years ago by sbrown66920 • updated 2.9 years ago by montoya.oscar50

Latest awards to sbrown669

Popular Question 3.4 years ago, created a question with more than 1,000 views. For PANTHER gene ontology - is the bonferroni correction important?
Popular Question 3.4 years ago, created a question with more than 1,000 views. For cutadapt loop and paired-end reads

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