Q10. When I try to perform Principal Component Analysis (PCA) during QC or Analysis I get the following error message: “cube.strandgenomics.ani.SharedMonitorModel.createNativeSharedObject()J”. How can this be resolved?

This error indicates that some of the required library files are not present. To install the necessary library files, go to the app/msvc_redist folder in the GeneSpring installation directory and double-click the appropriate msvc_redist file for your system specifications:

  • vcredist_x86 for a 32-bit system
  • vcredist_x64 for a 64-bit system.

Accept the License Agreement by clicking Yes.

Q1. In 'Quality control on samples', the option to 'Add/Remove' samples is grayed out. Why?

The option of 'Add/Remove' samples is grayed out as it is not supported for a Generic single color or Generic two color experiment.

Q2. For how many samples does GeneSpring display "Correlation Coefficients" and "Correlation plot" on Quality control on samples?

The maximum number of samples for which the correlation coefficient plot can be shown is 100. This is because it is a compute intensive operation.

Q3. Why is the Correlation plot removed from 'Quality Control on Samples' window for Agilent Two color technology in GeneSpring.

In earlier versions of GeneSpring , only Cy3 channel values were being considered to show the correlation plot for two-color data. Currently we are considering the ratio between Cy3 and Cy5 channels. So, it is not an appropriate method of judging correlation between samples, since weightage needs to be given to both the channels. Hence, the correlation plot is unavailable in two-color Quality Control window in GeneSpring.

Q4. Please give me some information about the 'Filter on Parameter'.

Filter on Parameters calculates the correlation between expression values and parameter values.
It requires a numerical parameter with which a profile is created and then correlated to profiles of the entities present in the selected Entity List.
The profile of the entities is based on their expression values accorded to them based on their interpretation.

Q5. I am working with Affmetrix data. I cannot use Filter on Flags. Why?

With Affymetrix data, the Filter by Flags is not applicable if you are working with .CEL files and Summarization algorithm other than MAS 5.0.

With text files, please select the flag column during data import to use this feature.

Q6. I would like to use Filter by Flags functionality for Affymetrix data. Is it possible?

The Filter by Flags functionality for Affymetrix data could be used when you are working with .CHP files. The CHP files contain the flag information.

If you are working with .CEL files then use MAS 5.0 summarization to generate the Flags.

Q7. Why is the default percentile set to '20' in the 'Filter probe set by expression option'? Also, how does changing the number of samples make a difference to the filtering results?

There are two factors based on which the filtering is done here. The percentile cutoff and the filter criteria of in how many samples must a probe set have intensity value within the specified range. Together, these two factors will determine what kind of probe sets is eliminated.

Factor 1: Percentile cutoff

Q8. What does filter probe sets by flags mean?

Flags are attributes that denote the quality of the entities. Using these attribute values in GeneSpring we filter the genes.
These values are generated based on the feature quality on the chip, like signal saturation and signal uniformity.
The genes which are given low significant attribute in the data file would be marked as 'Absent' and high significant values would be marked as 'Present'.

Q9. Where can I get the information about the columns that are used for the analysis in GeneSpring?

This information can be viewed by selecting the Filter on Data files option under Quality Control.

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