Q15. How can I analyze the Opticon Superarray RT-PCR data with GeneSpring?

GeneSpring currently supports only RQ 1.2, RQ 2.1 , RQ 2.2 and RQ 2.3 formats of the ABIs 7900HT RT-PCR data as a Standard format.
However, to work with SuperArray qRT-PCR data, you need to create a custom single color technology using the path below:
GeneSpring GX Menu Bar → Annotations → Create Technology → Custom From File
You could then import the data by creating an experiment by selecting the Experiment Type as Generic Single Color. Please specify 'Detector' column from the file as the identifier column.

Q16. When I tried to import the GPR file, I got the error "Unable to Process the Supplied Data. Beginning of the Data not Found"

GeneSpring supports the creation of GPR technology ( Annotations → Create Technology → From .gpr file) only for the two color GPR data.
The two color .GPR file used to create the technology should contain the following columns - ID, F635 Median - B635, F532 Median - B532, and Flags.
In the absence of the above specified columns, the error would be seen.

Q17.Can I import .GPR files in GeneSpring?

Yes, .GPR files could be imported into GeneSpring.
Please find the details below:
Two color array:
A) Two color .GPR files from Agilent standard array could be imported by selecting the “Agilent two color” as the experiment type in the ‘New Experiment’ window for the standard workflow.
B) Two color .GPR files from custom array could be imported by following the steps below:

Q18. Can we add new samples to the existing experiment?

Currently, the option to add samples to an existing experiment is unavailable. To add a new sample into an experiment, create a new experiment by including that sample with the rest of the samples.

Q19. How can we delete the CEL files that were already used for creation of experiments?

Samples can only be deleted by deleting the experiments associated with them.
Experiments can be deleted using the path below: GeneSpring menu bar -> Search -> Experiments -> In the search wizard select the experiments to be deleted -> Select the ‘Delete’ icon Note: Once the sample is deleted from all the associated experiments, those experiments cannot be accessed.

Q20. The microarray experiment was performed in another lab and I do not have enough information to recognize the samples. Where can I find the sample related information for identification of the sample in GeneSpring?

After experiment creation, the sample information can be found in ‘Sample Inspector’.
Use right click on the sample name in ‘Experiment Navigator’ and select ‘Inspect Sample’ option to launch the inspector.
The Attributes, Parameters and Associated files information is shown in this window.

Q21. I would like to import datasets from NCBI. However, the option ''Import NCBI GEO Experiment'' is disabled? How could I enable it?

The Import NCBI GEO Experiment option is available only when an experiment is active under a Project. Open a Project followed by an Experiment in GeneSpring for the data import.

Q22. I have just installed GeneSpring 12.x on a new machine. Is it possible to transfer data and analysis from my old computer running GeneSpring GX 10.x/11.x to this new machine. Is there an Import tool or do I just transfer the folder with the data?

To transfer the data from one machine to another machine, export the data as Project zips from GeneSpring GX 10.x/11.x and import it into latest version of GeneSpring. This could be done from GeneSpring menu bar --> Project --> Export project zip/Import project.
Copying the data folder from one machine to another machine does not allow the data transfer.

Q23. I am working with Illumina group probe profile data file and I get an error. How can I load my data into GeneSpring?

GeneSpring supports the data files generated from BeadStudio in GeneSpring format to create standard Illumina single color experiment.
One could export the results from BeadStudio into a variety of formats compatible with other commercially available analysis tools.
To work with Illumina files in GeneSpring, export the files in GeneSpring format. This could be done from Analysis --> Report --> Custom Report --> GeneSpring format.

Q24. I get an error "No such file or directory " while trying to load my data. What should I do?

The error ""No such file or directory " would occur if the row header in the data file has "/".
Hence, please replace "/" with "_" or with any non-special character to import the data into GeneSpring.
This should help you to import the data into GeneSpring.

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