FAQ

Frequently Asked Questions

 

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ArrayStar


General 

» How can I change my font settings within ArrayStar? 

The font used within ArrayStar is controlled by your Windows font settings for the "message box" item. To adjust these settings:


On Windows 7 and Windows 8:
  1. 1. Open the Control Panel.
  2. 2. Use the View by drop-down menu to view items by Small icons or Large icons.
  3. 3. Click on Fonts.
  4. 4. Using the links on the left, change the font settings and size to suit your preferences.
  5. 5. After making each change, click Apply.
On Windows XP:
  1. 1. Open the Control Panel.
  2. 2. Choose Display.
  3. 3. Select the Appearance tab.
  4. 4. Click the Advanced button.
  5. 5. Select "message box" from the Item list.
  6. 6. Change the font settings to suit your preferences.
  7. 7. Click OK, and then click Apply.

Your new font settings should now be reflected in ArrayStar.

» Why does an asterisk appear after my project name? 

When you have made changes to your project that have not yet been saved, an asterisk will appear after your project name in the ArrayStar title bar, as shown below:



Once you save the project, the asterisk will no longer appear, until further changes are made:



» What does a dash represent as a value in the Gene Table? 

In the Gene Table view, if a statistical calculation does not yield a valid result, a dash will be displayed in place of a numerical value.

» How do I cluster the experiments in my project? 
By default, the experiments in your project as well as the genes you have selected are clustered when you choose to do a Hierarchical Clustering. The option can be turned on and off by using the Clustering Parameters dialog. Access this dialog by selecting Clustering>Advanced Clustering.

Check the box next to Cluster Experiments if you would like to perform clustering on your experiments as well as the genes you have selected. Experiment clusters are displayed in the Experiment Tree in the Heat Map view.

Define which experiments should be clustered by selecting them from the list provided on the right side of the Clustering Parameters window.

To cluster individual experiments, rather than the averaged experiments within a replicate set, simply select the checkboxes next to the individual experiments, rather than the replicate set name.

Note that genes must have binding activity in at least some of their conditions in order to be clustered. In a ChIP-Seq project, most of the genes do not have binding activity near them, so clustering such genes is not a valid operation. To make an appropriate ChIP-Seq gene selection, you may wish to try selecting genes from the Scatterplot rather than the Gene Table.
» How do I remove all of the columns in the Gene Table? 
You can remove individual columns from the Gene Table by right-clicking on the column header and choosing Remove Column. However, if you wish to remove all of the columns that you have added to your Gene Table, simply close the Gene Table and reopen it.

By default, all of the data in your project defined as Gene IDs will be displayed each time you open a new Gene Table.
» The gray highlight is too hard to see on Windows 7 or Windows 8. How can I make it darker? 
You can change the personalization settings to make the highlight color easier to see.

To adjust this setting on Windows 7 or Windows 8:

1. Open the default Windows Control Panel.
2. Select Appearance and Personalization.
3. Select Change the theme.
4. Choose a high-contrast theme and apply the changes.

An alternative method of adjusting this setting on Windows 7:

1. Open the default Windows 7 Control Panel.
2. Select Appearance and Personalization.
3. From the Personalization category, select Change window glass colors.
4. Click on the Advanced appearance settings hyperlink.
5. From the Item drop-down menu, select Inactive Window Border.
6. From the Color drop-down menu, choose a color to suit your preferences.
7. Click Apply, then OK. Finally, click the Save changes button.

Your new highlight color should now be reflected in ArrayStar.

» Can I import a Final Report from BeadStudio? 
Yes. Final Reports from Illumina's BeadStudio software can be imported into ArrayStar as long as the necessary criteria was selected when it was saved.

To prepare a Final Report in BeadStudio to be imported into ArrayStar:

1. Make sure that Sample Gene Profile is selected in the Tables column.
2. Under Columns, select TargetID, at least one experiment, and any ontology information that you wish to import into ArrayStar.
3. Select AVG_Signal under Subcolumns.



After saving the Final Report, you can import it into ArrayStar by doing the following:

1. Select File>Import Experiments. The Project Setup Wizard will launch.
2. Click Add Data File and navigate to the Final Report text file you just saved.
3. Proceed as usual through the Project Setup Wizard to complete the import.
» Why does the ArrayStar SNP Table appear to contradict the SeqMan SNP Report in some cases? 
In the ArrayStar SNP Table, the column “Contig Pos” collapses all permutations for a given reference position into a single record with start and end positions separated by an ellipsis (e.g. 27…31). If multiple bases are listed, this indicates a multi-base insertion into the sample relative to the reference.

In most cases, the single record denotes that all included reference positions contain the same SNP. In some cases, however, the record may include one or more reference positions that do not have that SNP when the corresponding assembly is viewed in the SeqMan Alignment View or SNP Report.

This is due to a difference in how ArrayStar and SeqMan call SNPs. SeqMan checks the P value of each putative SNP. If a SNP has a roughly 50% chance of not being a change, it is not included in SeqMan’s Alignment View or SNP Report. That’s because there are often low-probability columns present due to sequencing errors or alignment issues, and these do not indicate an actual insertion. However, these “possible” SNPs are still included in the ellipsis-separated range of the “Contig Pos” column in ArrayStar.

The scores for ArrayStar’s “Contig Pos” records are aggregated as follows:
  • Depth: The mean depth among all of the columns considered.
  • SNP %: The mean percentage among all of the columns considered.
  • Q-call: The lowest confidence score among all of the columns considered.
  • P-value: The lowest probability among the columns passing the filter.
  • An indel in a translated regions is always considered a frameshift, unless it's a triplet, in which case it is considered non-synonymous.

    If any of the used columns was heterozygous, the entire record is considered heterozygous. The alleles are not correlated in the data used by ArrayStar, and so all combinations of the individual bases' alleles are possibilities unless manual investigation of the assembly shows otherwise.
    » How can I change the default printing size? 
    Unless otherwise specified on your computer, the default printing size for all DNASTAR applications is “U.S. Letter” size (8.5 x 11 inches = 21.6 x 28 cm). You can temporarily change to another size, such as A4, from within the application. However, the next time you print, the default size will again be U.S. Letter size.

    To correct this issue, you need to change your computer’s default printing size:

    Note: If you are a Macintosh user running ArrayStar on Parallels Desktop, adjust the printing size on the Windows side.

    On Windows 7 and Windows 8:
    1. 1. Open the Control Panel.
    2. 2. In the Hardware and Sound category, click on Printers or View devices and printers.
    3. 3. Right-click on your printer and choose Properties.
    4. 4. In the General tab, click on the Printing Properties button.
    5. 5. In the ensuing Printing Shortcuts tab, choose the desired default printing size from the Printing Sizes drop-down menu.
    6. 6. Click the Apply button, then the OK button.
    Note: Changes to the default printing size will not be applied until after you restart the DNASTAR application.

    ArrayStar Troubleshooting 

    » Why can't I see certain values in my search results? 

    The columns displayed in your Search Results pane, shown in the bottom half of the Advanced Filtering window, are controlled by your Gene Information Settings. In order to view fold change, statistics, and expression level values for the genes found in your search results, click the  button from the toolbar, and then go to Data>Show Gene Table. Once you are in the Gene Table, it may be necessary to click the  button from the Gene Table toolbar to display only your search results.

    » Why can't I click "Calculate" in the Statistics Parameters window? 

    The Calculate button will only be enabled when the selection of experiments is valid for the chosen statistical test.


    Statistical analyses can be performed only on replicate sets within your project, not on individual experiments. The experiments within each replicate set are displayed, but cannot be individually selected. You must select a replicate set or sets (depending on the test) before you will be able to calculate the results.

  • Only 1 replicate set may be selected to calculate Standard Deviation, Variance, or the Coefficient of Variation.
  • Only 2 replicate sets may be selected to calculate the Student's t-test or Moderated t-test.
  • At least 3 replicate sets must be selected to calculate the F-Test (ANOVA).
  • » Why do I receive an "Error: Loading..." message when trying to import my data? 

    If ArrayStar has difficulty importing your data, one of the following errors may appear:


    "The data file ... contains # duplicate genes within itself."


    This means that the data file cannot be loaded because a unique Gene ID has not been designated for each gene in your file. Try selecting additional columns as "Gene ID" in the Data Import Wizard. Or, open your delimited text file in a program such as Microsoft Excel, and add a column with a unique ID for each row in your file (such as 1, 2, 3, etc.). Then, designate your newly added column along with other columns containing gene identifiers as "Gene ID" during the import.


    "The data file ... contains # genes which are ambiguous with regard to the project."


    This error may occur when multiple files in your project have different columns designated as "Gene ID" and some of the genes in one file match multiple entries in another.


    At least one Gene ID column in the data file you are importing must match with the Gene ID chosen for the existing datasets in your project. Make sure you selected the correct file to import and designated the correct column(s) as "Gene ID." If necessary, manually edit your file in a program such as Microsoft Excel to add a new Gene ID column that matches the existing Gene IDs in your project. Then, designate your newly added column along with other columns containing gene identifiers as "Gene ID" during the import.


    "The data file ... contains # genes, none of which match the genes already loaded in the project."


    This means that none of the data in the file being imported matches the data that is already in your project.


    At least one Gene ID column in the data file you are importing must match with the Gene ID chosen for the existing datasets in your project. Make sure you selected the correct file to import and designated the correct column(s) as "Gene ID." If necessary, manually edit your file in a program such as Microsoft Excel to add a new Gene ID column that matches the existing Gene IDs in your project. Then, designate your newly added column along with other columns containing gene identifiers as "Gene ID" during the import.

    » Why are some of my genes missing values? 
    Occasionally, you may see a message in the Details section of the Experiment List view notifying you that some genes are missing.

    For example: "There are 516 genes missing values out of 6847 genes in this experiment. You may wish to create a replicate set to compensate for the missing data."

    This message may appear for one of the following reasons:

  • The annotation file imported for your project contains annotations for genes that are not present in your experiments. If this is unexpected, importing the correct annotation file should solve the problem. Or, if you imported annotations through the Data Import Wizard, first verify that you designated the correct columns during the import, and then re-import if necessary.

  • Some of the chips in your project contain genes that are not present on other chips in the same project. If this is unexpected, importing the correct data file should solve the problem. Or, if you imported your data through the Data Import Wizard, first verify that you designated the correct columns during the import, and then re-import if necessary.

  • Some of the genes in your project do not have expression level values associated with them. You can look in the Gene Table to find genes that are missing values. Genes without expression levels will show --- in place of values. In this case, it may be beneficial to add more replicates if possible, and then group your replicates into replicate sets. The averaging method that you select for each replicate set (mean or median) will determine how the missing values are handled. In both cases, the missing replicates will not be counted for that gene. In mean averaging, any gene that has no value in one or more replicates will cause the other replicates to have more weight for that gene.
  • » Why do my statistical analysis results in ArrayStar differ from my results in another program? 
    Differences in statistical results between ArrayStar and another program can be due to many factors. However, when making a comparison, it is important to confirm that the parameters used for both analyses are the same.
    Two important factors to note:
    • » ArrayStar always uses the log2 of expression values for statistical analysis.
    • » By default, FDR is used as the multiple testing correction method. You may change the method or perform an uncorrected test by changing the statistics parameters used.
    When the parameters used in both tests are the same, the results in ArrayStar should correspond to the results obtained from other statistical programs.
    » Why can't I "Create Sets" in the Create Temporary Sets dialog? 
    The Create button will only be enabled in the Create Temporary Sets dialog when all of the following criteria are met:
  • The selected experiments contain valid gene values.
  • A maximum P-value or minimum Fold Change is specified. If you pick Fold Change, you must specify Up, Down, or both.
  • Multiple sets are selected so that pairwise comparisons may be made.
  • » Why do I receive an error message during data file import? 
    While importing data sets into ArrayStar, you may receive the following error message:

    There was an error while importing. Cannot access a disposed object. Object name: 'ProjectSetupWizard'.

    This error indicates that you do not have enough RAM to import the data file in question. In general, more RAM is needed to import text files vs. SeqMan NGen projects, or whole-genome data sets vs. smaller data sets. To close the message, click OK.
    » Why do I receive an error message when I try to launch ArrayStar? 
    If you recently installed ArrayStar, you may encounter an error message and be prevented from opening the application. This issue can occur if your computer does not have the .NET Framework 3.5 Service Pack 1 installed.

    To resolve this issue, run Windows Update and install the .NET Framework 3.5 Service Pack 1 .