What is GCT file format?
GCT (Gene Cluster Text) is a tab-delimited text file format that is convenient for analysis of matrix-compatible datasets as it allows metadata about an experiment to be stored alongside the data from the experiment. GCT files enable storing both row and column metadata.
What can you do with microarray data?
Microarrays can be used in many types of experiments including genotyping, epigenetics, translation profiling and gene expression profiling. Gene expression profiling is by far the most common use of microarray technology. Both one- and two-colour microarrays can be used for this type of experiment.
What is Affymetrix microarray data?
The Affymetrix GeneChip system is a commercial microarray platform that allows whole genome gene expression analysis for a wide variety of experimental organisms (http://www.affymetrix.com/products/arrays/index.affx).
How do I save a GMT file?
When saving the file, make sure you save the file as a tab delimited text file, and type the extension . gmt at the end of the filename. If you see in the file manager that excel has added . txt after .
How do I create a GMX file?
To create a GMX file, select File → New Project, name the file, choose the save location, and click Save. To open a GMX file, select File → Open Project…, navigate to your file, and click Open.
How do I open a chip file?
If you want to view the spreadsheet data a CHIP file contains, you can open the file in Microsoft Excel (Windows, Mac).
What conclusions can you make from microarray data?
Microarray data allows you to determine the level of gene expression in a patient for many genes at one time. In this case, the data provides some insight into which genes may be affected in the development of cancer. 7. In some cancer cells, mRNA is produced (as it would be in a normal cell).
What is the difference between RNA Seq and microarray?
The main difference between RNA Seq and microarray is that the RNA Seq (RNA Sequencing) allows analyzing novel RNA and RNA variants whereas the microarray allows analyzing the transcriptome with the use of known RNA probes. Furthermore, RNA Seq is a sequencing-based technique while microarray is based on hybridization.
How do Illumina microarrays work?
How Do Illumina Microarrays Work? As DNA fragments pass over the BeadChip, each probe binds to a complementary sequence in the sample DNA, stopping one base before the locus of interest. Allele specificity is conferred by a single base extension that incorporates one of four labeled nucleotides.
How do you cite GSEA?
To cite GSEA, please reference Subramanian, Tamayo, et al. 2005 Proc Natl Acad Sci U S A 102(43):15545-50. To cite your use of the Molecular Signatures Database (MSigDB), please reference Liberzon et al. 2011 Bioinformatics 27(12):1739-40 and also the source for the gene set as listed on the gene set page.