RNA-Seq Pathway and Gene-set Analysis Workflows in R/Bioconductor with GAGE/Pathview

[entrez]

I’ve both gage and pathview installed on my computer. I tried to follow the example in the native workflow. Things work well, except I didn’t get 4 samples show up in the same graph (or nodes with 4 slices) as in Figure 2 of the workflow document, instead I got 4 separate graphs. What I might have done wrong?

[bigmw]

GAGE and Pathview can be used independent of each other. GAGE does pathway and Gene-set Analysis, and works on other tyeps of gene sets than pathways, like GO, coexpressed/coregulated gene sets, TF or miRNA target lists etc. Pathview may integrate and visualizeuser data onto pathway graphs independent of pathway analysis procedure.

Pathview package available at:

http://bioconductor.org/packages/release/bioc/html/pathview.html

Here is the info page with example output:

http://pathview.r-forge.r-project.org/

[bigmw]

The gage package (2.12.0) now includes a new tutorial, "RNA-Seq Data Pathway and Gene-set Analysis Workflows". Note you need to update to current release versions of R(3.0.2)/ Bioconductor(2.13) to use all the features. Please check it out:

http://bioconductor.org/packages/release/bioc/html/gage.html

http://bioconductor.org/packages/release/bioc/vignettes/gage/inst/doc/RNA-seqWorkflow.pdf

We first cover a full workflow from preparation, reads counting, data preprocessing, gene set test, to pathway visualization in about 40 lines of codes. The same workflow can be used for GO analysis or other types of gene set analysis too. We also describe joint workflows, i.e. to do gene-level analysis using one of the major RNA-Seq analysis tools, DEseq/DEseq2, edgeR, limma and Cufflinks, and feed the results into GAGE/Pahview for pathway analysis or visualization. All these workflows are implemented in R/Bioconductor.
Comments and questions are welcome. Thanks!