Frequently Asked Questions
The option of 'Add/Remove' samples is grayed out as it is not supported for a Generic single color or Generic two color experiment.
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.
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.
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.
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.
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.
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
We try to set this percentile cutoff to only eliminate genes that are not expressed. What we are saying is that if an intensity value of a probe set is below the 20th percentile in that sample, the gene is probably not expressed in that sample. It is known that any given tissue, not all genes in the human genome is expressed. On average across different types of tissues, we can expect that 20% of the genes are not expressed. Therefore, you can expect that about 20% of the probe sets on any given genome-wide array (sample) have intensity values that represent noise (since they are not expressed).
Factor 2: Number of samples
If probe sets were filtered such that they must have values within the range (above 20th percentile) in all samples (or in both conditions), then there is a possibility of interesting genes being excluded. Thus, potentially interesting biological changes between experimental conditions could be missed. To decrease the chances of missing these changes, the stringency of the filter is set such that even if the gene is only expressed in one sample in the experiment, the probe set will pass the filter. But, this criterion could be changed by the user according to their interest.
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'.
These flags are generally specific to the technology or the array type used. Thus the experiment technology type, i.e., Agilent Single Color, Agilent Two color, Affymetrix Expression, Affymetrix Exon Expression, and Illumina Bead technology determine the flag notation.
This information can be viewed by selecting the Filter on Data files option under Quality Control.
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.
The missing libraries are installed. You need to restart GeneSpring for the changes to take effect.