Recent changes to expression_cor

expression_cor modified by Keith Ching

Keith Ching — Mon, 23 May 2016 21:23:18 -0000

--- v4
+++ v5
@@ -13,6 +13,7 @@
 Plot heatmap : checkbox whether to plot a heatmap (default unchecked)
 All TCGA : checkbox to calculate the same correlation across each and every TCGA dataset and summarize the results. (default unchecked)
 colors for heatmap metadata: colors for metadata categories when plotting heatmap with meta data (default red blue green violet orange yellow black)
+(Dev) Split dataset by metadata: (default unchecked) Do the correlation on each subset of data as defined by the metadata category. eg. LumA, LumB, Her2, Basal subtype.  Generates a concatentated list of scores labelled by meta type. If heatmap, then one file with one heatmap for each meta type.

 for technical details see: [genefilter](http://www.bioconductor.org/packages/release/bioc/html/genefilter.html)

expression_cor modified by Keith Ching

Keith Ching — Tue, 10 Mar 2015 18:05:37 -0000

--- v3
+++ v4
@@ -15,7 +15,7 @@
 colors for heatmap metadata: colors for metadata categories when plotting heatmap with meta data (default red blue green violet orange yellow black)

-for technical details see: [genefu](http://www.bioconductor.org/packages/release/bioc/html/genefu.html)
+for technical details see: [genefilter](http://www.bioconductor.org/packages/release/bioc/html/genefilter.html)

-Haibe-Kains B, Schroeder M, Bontempi G, Sotiriou C and Quackenbush J (2014). genefu: Relevant Functions for Gene Expression Analysis, Especially in Breast Cancer.. R package version 1.16.0, http://www.pmgenomics.ca/bhklab/.
+Gentleman R, Carey V, Huber W and Hahne F. genefilter: genefilter: methods for filtering genes from high-throughput experiments. R package version 1.48.1.

expression_cor modified by Keith Ching

Keith Ching — Sat, 31 Jan 2015 00:17:54 -0000

--- v2
+++ v3
@@ -15,7 +15,7 @@
 colors for heatmap metadata: colors for metadata categories when plotting heatmap with meta data (default red blue green violet orange yellow black)

-for technical details see: (genefu)[http://www.bioconductor.org/packages/release/bioc/html/genefu.html]
+for technical details see: [genefu](http://www.bioconductor.org/packages/release/bioc/html/genefu.html)

 Haibe-Kains B, Schroeder M, Bontempi G, Sotiriou C and Quackenbush J (2014). genefu: Relevant Functions for Gene Expression Analysis, Especially in Breast Cancer.. R package version 1.16.0, http://www.pmgenomics.ca/bhklab/.

expression_cor modified by Keith Ching

Keith Ching — Sat, 31 Jan 2015 00:17:29 -0000

--- v1
+++ v2
@@ -13,3 +13,9 @@
 Plot heatmap : checkbox whether to plot a heatmap (default unchecked)
 All TCGA : checkbox to calculate the same correlation across each and every TCGA dataset and summarize the results. (default unchecked)
 colors for heatmap metadata: colors for metadata categories when plotting heatmap with meta data (default red blue green violet orange yellow black)
+
+
+for technical details see: (genefu)[http://www.bioconductor.org/packages/release/bioc/html/genefu.html]
+
+Haibe-Kains B, Schroeder M, Bontempi G, Sotiriou C and Quackenbush J (2014). genefu: Relevant Functions for Gene Expression Analysis, Especially in Breast Cancer.. R package version 1.16.0, http://www.pmgenomics.ca/bhklab/.
+

expression_cor modified by Keith Ching

Keith Ching — Sat, 31 Jan 2015 00:15:46 -0000

[Instructions]

Find which genes are correlated with the selected gene(s).

HUGO : gene symbol(s) to correlate to (required)
EXPRESSION : source of expression data (required)
METADATA : optional
gene num results : number of genes to return (required) (default 25)
direction : both/positive/negative sign of correlation to return (default both)
gene scaling : whether to scale genes before correlation none/range/z-score (default none)
distance metric : how to calculate similarity correlation/euclidean/maximum/manhattan/canbera/binary (default correlation)
Plot heatmap : checkbox whether to plot a heatmap (default unchecked)
All TCGA : checkbox to calculate the same correlation across each and every TCGA dataset and summarize the results. (default unchecked)
colors for heatmap metadata: colors for metadata categories when plotting heatmap with meta data (default red blue green violet orange yellow black)