Changes between Version 1 and Version 2 of SOPs/diff_rnaSeq

Timestamp:

01/25/13 09:37:18 (12 years ago)

Author:

gbell

Comment:

--

SOPs/diff_rnaSeq

@@ -33 +33 @@
   * Input for edgeR should be a matrix of counts, not RPKM values.
     * From the edgeR manual: "RPKM values should not be used for assessing differential expression of genes between samples in edgeR. We use the raw counts, because the methods implemented in edgeR are based on the negative binomial distribution, a discrete distribution."
-  * See [[http://iona.wi.mit.edu/bio/bioinfo/Rscripts/get_DE_genes_with_edgeR.R|get_DE_genes_with_edgeR.R]] for a command-line script to use edgeR
+  * See [[http://jura.wi.mit.edu/bio/scripts/R/get_DE_genes_with_edgeR.R|get_DE_genes_with_edgeR.R]] for a command-line script to use edgeR
   * Major edgeR upgrade (April 2010?) required a change from version 0.1 to 0.2 of above script.
   * Outputs also includes image files: boxplot, MA plot, volcano plot
@@ -106 +106 @@
   * 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
@@ -125 +125 @@
   * [[http://www.ncbi.nlm.nih.gov/pubmed/20979621|DESeq ("Differential expression analysis for sequence count data")]] - Anders S, Huber W. Genome Biol. 2010;11(10):R106. Epub 2010 Oct 27.
   * [[http://bioinfo.cipf.es/noiseq/doku.php?id=tutorial|NOISeq]]
-  * 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 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 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 ]
   * You may also want to check this SOP: [wiki:SOPs/rna-seq-diff-expressions/ Using RNA-Seq to quantify gene levels and assay for differential expression]