Genespring

8-6-13 Note that our lab will not continue the license for Genespring any longer. I think there are about 15 days left on the license.

I copied all of the gene lists and experiments out of genespring into excel files. All of this data as of 8-6-13 can be found here. All Genespring data as of 8-6-13

"F:\kurt\storage\CIM Research Folder\DR\2013\8-6-13\All Kurt Genespring Data as of 8-6-13"

- Genespring GX 7.3 Manual



-- Instructions for starting to analyze some slides with GeneSpring (We have Genespring GX 7.3)

To point genespring to your data: go to preferences and set the folder as research->doc-in-a-box->genespring make sure the correct “genome” is selected

RemoteDesktop: bio4043444 (Note that the Genespring computer is a remote server that many people can remote to) Make sure it says Alta10k File->Open Genome or Array->Data->Alta10K (if it does not say Alta10k array at the top of the screen) Custom->Alta10K Array <span style="background-color: #ffffff; color: #000000; font-family: Verdana; font-size: 13px; text-decoration: none; vertical-align: baseline;">Drag gpr files onto program
 * other arrays opened recently: 3K_lysate_3-2-12

<span style="background-color: #ffffff; color: #000000; font-family: Verdana; font-size: 13px; text-decoration: none; vertical-align: baseline;">Name->Gene Identifier <span style="background-color: #ffffff; color: #000000; font-family: Verdana; font-size: 13px; text-decoration: none; vertical-align: baseline;">Median->Signal <span style="background-color: #ffffff; color: #000000; font-family: Verdana; font-size: 13px; text-decoration: none; vertical-align: baseline;">Flags->Flags <span style="background-color: #ffffff; color: #000000; font-family: Verdana; font-size: 13px; text-decoration: none; vertical-align: baseline;"> Present Flag: 0 <span style="background-color: #ffffff; color: #000000; font-family: Verdana; font-size: 13px; text-decoration: none; vertical-align: baseline;"> Absent Flag: -100 <span style="background-color: #ffffff; color: #000000; font-family: Verdana; font-size: 13px; text-decoration: none; vertical-align: baseline;"> Marginal Flag: -100

<span style="background-color: #ffffff; color: #000000; font-family: Verdana; font-size: 13px; text-decoration: none; vertical-align: baseline;">Next

<span style="background-color: #ffffff; color: #000000; font-family: Verdana; font-size: 13px; text-decoration: none; vertical-align: baseline;">Click normalize button. Delete the option that says something like "per gene: normalize to median " and keep the option that says something like "per chip: normalize to 50th percentile"

To make histograms Right click experiment, and set parameter name to non-continuous for a histogram and to continuous for a line graph. Then choose View->Graph->Line Graph. The axis may need to be adjusted to see the histograms in view.

Genespring out of memory error

Genespring heatmaps

creating a new genome in genespring

Our lab will stop paying for the license for GeneSpring. There are about 45 days left as of 7-25-13