Changes between Version 1 and Version 2 of SOPs/rna-seq-diff-expressions

Timestamp:

01/25/13 09:48:23 (12 years ago)

Author:

gbell

Comment:

--

SOPs/rna-seq-diff-expressions

@@ -66 +66 @@
      * As with microarray normalization, be aware of the assumptions of each method and choose the method(s) which are most valid with your experiment
      * Origin of recommendation for upper-quartile normalization: [[http://www.ncbi.nlm.nih.gov/pubmed/20167110|Bullard et al., 2010]]
-     * See [[http://iona.wi.mit.edu/bio/bioinfo/Rscripts/normalize_DGE_matrix.R|normalize_DGE_matrix.R]] for a command-line script for count normalization
+     * See [[http://jura.wi.mit.edu/bio/scripts/R/normalize_DGE_matrix.R|normalize_DGE_matrix.R]] for a command-line script for count normalization
        * Methods for above script: mean, median, quantile, percentile, none
        * Outputs also includes before and after image files: boxplots, scatterpots, violin plots
@@ -114 +114 @@
       * [[http://www.ncbi.nlm.nih.gov/pubmed/21106489|A survey of statistical software for analyzing RNA-seq data]] - Gao D, Kim J, Kim H, Phang TL, Selby H, Tan AC, Tong T.  Hum Genomics. 2010 Oct;5(1):56-60.
       * [[http://www.ncbi.nlm.nih.gov/pubmed/21176179|From RNA-seq reads to differential expression results]] - Oshlack A, Robinson MD, Young MD.  Genome Biol. 2010;11(12):220. Epub 2010 Dec 22.
-   * For more practical information, see the third session of [http://iona.wi.mit.edu/bio/education/R2011/ | An introduction to R and Bioconductor: A BaRC Short Course] and the BaRC Hot Topic [http://jura.wi.mit.edu/bio/education/hot_topics/RNAseq/RNAseqDE_Dec2011.pdf | RNA-seq: A practical guide to the analysis of differential gene expression ]
+   * For more practical information, see the third session of [http://jura.wi.mit.edu/bio/education/R2011/ | An introduction to R and Bioconductor: A BaRC Short Course] and the BaRC Hot Topic [http://jura.wi.mit.edu/bio/education/hot_topics/RNAseq/RNAseqDE_Dec2011.pdf | RNA-seq: A practical guide to the analysis of differential gene expression ]