Q25. I am trying to import data into GeneSpring, however it gives an error "The system cannot find the path specified ". How can I import the data into GeneSpring?

"The system cannot find the path specified " would occur if the row header in the data file has "\" .
Please replace "\" with "-" to load the data in GeneSpring and create an experiment.
With these changes Genespring would recognize the files and import it to create an experiment.

Q26. Which characters are considered as special characters for data import in GeneSpring?

Following characters are considered as special characters in the tool: ! * # ; ? \ / : " < > |

Q27. I am working with a standard rechnology. During experiment creation GeneSpring gives "Invalid Column.Sizes do not match" error. What should I do?

The error could come up if the technology was earlier created on the fly due to loss of internet connections. This could result in difference in number of rows in the technology created on fly and the one present on the server.

Q14. I am working with copy number analysis. However, at the end of experiment creation it says "Error :-1". What could be the reason for this and would it affect my analysis?

The possible reason for "Error: -1" in copy number analysis could be the presence of "space" in the sample name.
Yes, it would affect the analysis. For example, running copy number analysis would not generate any output. Hence, please remove "space" from sample name for the successful experiment creation.

Q13. I have one project for Association study with 3 experiments (50 samples each). Now I would like to analyze all the 150 samples together. How I can merge the 3 experiments in GeneSpring?

In GeneSpring, currently it is not possible to merge multiple experiments to create a single experiment.
Create another experiment using all these 150 samples from three different experiment by selecting the Choose Samples option in the data loading step.
Note: Once the data files are imported into GeneSpring GX to create an experiment, the data files are converted into samples and would be stored in the database. If the Choose files option is selected again, then the sample is created the second time which utilizes twice the space in the database.

Q12. Is it possible to do CNV analysis with custom made arrays?

In GeneSpring, Affymetrix and Illumina data files are supported as standard formats.
Data files in other formats can be converted to the Standard Illumina format and imported into GeneSpring to perform the CNV analysis.
The mandatory columns to be present in the data file to create the technology are dbSNPID, Chromosome Name, Chromosome Position, CNV regions in the same order.
From the data file, GeneSpring directly uses the following values for each sample.

Q11. How could I analyze the Affymetrix miRNA chips in GeneSpring, if the data files are in txt, csv and xls format?

To load Affymetrix miRNA data files in txt, csv and xls format, create a Custom Technology ( Annotations-> Create Technology ->Custom from File). Then, import the files under 'Generic Single Color' experiment type.
To perform the 'Target Scan analysis', select the option 'TargetScan' in the Results Interpretations from Workflow Browser.

Q10. I am trying to create Agilent miRNA experiment but I am getting the error 'All Agilent miRNA sample files need to have the same Grid_Date field'. All the samples are extracted from the chips with similar design Ids. What should I do?

In GeneSpring, the AMADID number field and the Grid_Date fields are considered as unique identifiers for miRNA arrays.
The Grid_Date field gives information on the version of the design file that was used to extract the data during sample creation. This means that even if the AMADID number is same for the same sample (for example: 19118), if they were created using a different design file, then they will not be taken together for experiment creation.
If the data set includes files from different Grid_Dates, you can create a custom technology to analyze them together.

Q8. Do we have standard technologies in GeneSpring for miRNA data analysis?

Yes, There are few standard Agilent miRNA technologies available on GeneSpring update server. Please download the approprite technology from GeneSpring update server before you try to load the data for analysis.
Please contact us for any specific technology you are working with which is not available on update server.

Q7. What type of data files does GeneSpring support for miRNA analysis?

GeneSpring supports the Agilent single color miRNA data files from Feature Extraction software, version 8.5 or later version.
In case the user has files in any other format, a Custom technology and a Generic experiment could be created in GeneSpring to perform miRNA analysis.

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