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Creator:

Peter Li

Microarray data analysis using R

Created: 02/07/08 @ 11:30:06 | Updated: 02/07/08 @ 11:30:06

2 items in this pack

Comments: 0 | Viewed: 147 times |

Uploader:

Paul Fisher

A Taverna Users Guide

Created: 04/08/08 @ 17:40:21 | Updated: 04/08/08 @ 17:40:21

Credits: Paul Fisher Katy Wolstencroft Franck Tanoh

License: Creative Commons Attribution-Share Alike 3.0 License

File type: application/vnd.ms-powerpoint

Rating: 0.0 / 5 (0 ratings) | Comments: 0 | Viewed: 61 times | Downloaded: 58 times

Uploader:

Paul Fisher

HUMAN Microarray CEL file to candidate pathways (v4)

Created: 03/10/07 @ 18:35:55 | Updated: 04/04/08 @ 12:14:20

License: Creative Commons Attribution-NoDerivs 3.0 License

This workflow takes in a CEL file and a normalisation method then returns a series of images/graphs which represent the same output obtained using the MADAT software package (MicroArray Data Analysis Tool) [http://www.bioinf.manchester.ac.uk/MADAT/index.html]. Also retruned by this workflow are a list of the top differentialy expressed genes (size dependant on the number specified as input - geneNumber), which are then used to find the candidate pathways which may be influencing the observed ...

Rating: 5.0 / 5 (1 rating) | Versions: 4 | Reviews: 0 | Comments: 0 | Citations: 0

Viewed: 1365 times | Downloaded: 1293 times

Uploader:

Peter Li

Query Maxd microarray database (v1)

Created: 14/11/07 @ 16:01:50 | Updated: 22/11/07 @ 12:06:32

Credits: Peter Li

License: Creative Commons Attribution-Share Alike 3.0 License

Retrieves data from the maxd database given name of data set

Rating: 0.0 / 5 (0 ratings) | Versions: 1 | Reviews: 0 | Comments: 0 | Citations: 0

Viewed: 399 times | Downloaded: 428 times

Uploader:

Paul Fisher

Microarray CEL file to candidate pathways (v2)

Created: 08/02/08 @ 14:17:23 | Updated: 14/05/08 @ 15:43:16

Credits: Paul Fisher Saeedeh

License: Creative Commons Attribution-Share Alike 3.0 License

This workflow takes in a CEL file and a normalisation method then returns a series of images/graphs which represent the same output obtained using the MADAT software package (MicroArray Data Analysis Tool) [http://www.bioinf.manchester.ac.uk/MADAT/index.html]. Also retruned by this workflow are a list of the top differentialy expressed genes (size dependant on the number specified as input - geneNumber), which are then used to find the candidate pathways which may be influencing the observed ...

Rating: 0.0 / 5 (0 ratings) | Versions: 2 | Reviews: 0 | Comments: 0 | Citations: 0

Viewed: 598 times | Downloaded: 1 time

Uploader:

Pieter Neerincx

AffyArrayQualityAnalysis (v2)

Created: 13/03/08 @ 14:38:03 | Updated: 13/03/08 @ 14:40:37

Credits: Pieter Neerincx Philipg

License: Creative Commons Attribution-Share Alike 3.0 License

The AffyArrayQualityAnalysis web services provide quality control for raw Affymetrix GeneChip data. They are wrappers around Philip de Groot's quality control R script to provide remote programmatic access. This example workflow demonstrates the use of the AffyArrayQualityAnalysis services. The flow is as follows: * A client executes the AffyArrayQualityAnalysis_submit service with two inputs: a User object and a collection of URLs to CEL files. * The User object contains a user ID, a passw...

Rating: 0.0 / 5 (0 ratings) | Versions: 2 | Reviews: 0 | Comments: 0 | Citations: 0

Viewed: 388 times | Downloaded: 282 times

Uploader:

Peter Li

Identification of differential genes using t-tests by R (v2)

Created: 15/04/08 @ 15:37:42 | Updated: 01/07/08 @ 17:21:18

Credits: Peter Li

License: Creative Commons Attribution-Share Alike 3.0 License

This workflow starts by retrieving the names of microarray datasets from the Maxd database. The user has to select sets of control and test data for analysis using t-tests by R. A list of significant differentially expressed genes is then analysed using the Go Term Finder tool which generates a list of GO terms associated with the genes. A CSV file containing the list of significant genes is also generated.

Rating: 0.0 / 5 (0 ratings) | Versions: 2 | Reviews: 0 | Comments: 0 | Citations: 0

Viewed: 403 times | Downloaded: 238 times

Uploader:

Paul Fisher

Pathways from Diff Expressed Genes (v3)

Created: 03/10/07 @ 18:36:05 | Updated: 11/07/08 @ 10:52:01

License: Creative Commons Attribution-Share Alike 3.0 License

This workflow takes in probesets from and AffyMetrix micorarray experiment and returns: the genes in the QTL; gene start and end positions; chromosome where genes reside; ensembl trasncripts; SwissProt ids; affy probeset identifiers for chips Mouse430_2 and Mouse430a_2.

Rating: 5.0 / 5 (1 rating) | Versions: 3 | Reviews: 0 | Comments: 1 | Citations: 1

Viewed: 874 times | Downloaded: 799 times