Frequently Asked Questions
Please find the file formats supported in GeneSpring application for different Gene expression analysis Experiment Types below:
Affymetrix Expression, Affymetrix Exon Expression, Affymetrix Splicing Experiment Type/Affymetrix copy Number, Affymetrix Association analysis- .CEL / .CHP file format
Illumina Single Color, Illumina Copy Number/Illumina Association Analysis Experiment Type - .txt file format
Agilent Single Color, Agilent Two Color and Agilent miRNA Experiment Type: .txt file format
Pathway Experiment - .txt, .tsv, .csv and .xls
RT-PCR Experiment Type - RQ 1.2, RQ 2.1, RQ 2.2 and RQ 2.3 formats of the ABI's 7900HT RT-PCR system
Generic Single Color and Generic Two Color Experiment Type: .txt, .tsv, .csv and .xls
Note: Here in generic experiment, the user has an option to select the Identifier and the Signal column based on preference, unlike the above mentioned Standard Experiment Types.
Affymetrix text and pivot files can be loaded in GeneSpring 12.x as standard data and is associated to the standard technologies.
A. GeneSpring supports Affymetrix CEL and CHP files as standard format.
The other file formats such as .txt, .xls, .tsv and .csv are not recognised a standard file formats from affymetrix, but can be imported into GeneSpring for analysis.
You could work with .xls file by ‘Creating a Custom Technology’. To create a custom technology, follow the steps below:
1. Go to Annotations in the Menu bar -> Create Technology -> Custom from File
2. After creating the custom technology, you could create the experiment under ‘Generic Single color’ Experiment Type.
For more details please refer Chapter 13 & 14 on ‘Analyzing Generic Single color/Two Color Expression Data’ from the GeneSpring Manual.
This error occurs when special characters appear anywhere within the file path of the input CEL files. The workaround to resolve this error is to place the CEL files in a directory that does not have any special characters in the file path.
It really depends on what kind of samples you are working with. Please find the benchmarking table for GeneSpring version in the table below:
|Experiment Type||No.of samples||Memory used for experiment creation||Run time memory||Technology type|
|Agilent Single Color(Sample type-22K)||500||200M||300M||12097|
|Affymetrix Exon Splicing(RMA-Full)||50||583M||1009M||HuEx-1_0-st-V2|
|Affymetrix Exon Splicing(PLIER-Full)||50||570M||1009M||HuEx-1_0-st-V2|
|Affymetrix Exon Expression(RMA-Full)||50||187M||3589M||HuEx-1_0-st-V2|
|Affymetrix Exon Expression(PLIER-Full)||50||187M||3589M||HuEx-1_0-st-V2|
Note: Benchmarking for copy number and Association analysis are not included here.
You could get this error for the following reasons:
This error could occur while creating the experiment, if the ‘Experiment type’ chosen does not match the data files. Please select the right Experiment type and proceed with the analysis.
This error could also occur in case you are trying to import the data in an un-supported file format.
For Example: GeneSpring only supports the data files generated by Feature Extractor (FE) version 8.5 and later version. In case the data files generated by earlier versions of FE are imported, this error may occur. In this case you would need to bring the data files as custom data.
To work with custom data, create a custom technology before you load the samples into GeneSpring.
To create custom technology go to -> GeneSpring menu bar -> Annotations ->Create Technology -> Custom from File. For more details on custom technology creation, please refer the chapter 13 and 14 from GeneSpring manual.
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.
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.
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.
For more details on Custom or generic Single Color/Two Color data analysis, refer to the Chapter 13 and 14 in GeneSpring manual.
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.
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.
log R - Provides the log (base 2) ratio of the normalized R value for the SNP divided by the expected normalized R value.
BAF (B allele Frequency) Copy Number values and their confidences Genotype of the subject SNP for the sample along with the score.
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.
Sample probe profile file in GeneSpring export format will be supported by GeneSpring.
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.
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.
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.
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:
- Create GPR technology: The technology could be created using one of the files from, Annotations menu Create Technology From .gpr file Follow the wizard.
- After creating the technology, you would have to import all the files by creating an Experiment from the Project menu New Experiment Select Experiment Type as “ Generic Two Color”
Single color array:
To import single color .GPR files, please create a custom technology (Annotations Create Technology custom from file) followed by experiment creation from the Project menu New Experiment Select Experiment Type as “ Generic Single Color”
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.
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.
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.
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.
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.
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.
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.
"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.
Following characters are considered as special characters in the tool: ! * # ; ? \ / : " < > |
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.