Difference between revisions of "1001"
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<li>Contain more than the minimum number of genes. The minimum gene set size is set by the <span style="font-style: italic;">Min size </span>parameter (by default, 15).</li> | <li>Contain more than the minimum number of genes. The minimum gene set size is set by the <span style="font-style: italic;">Min size </span>parameter (by default, 15).</li> | ||
<li>Contain fewer than the maximum number of genes. The maximum gene set size is set by the <span style="font-style: italic;">Max size </span>parameter (by default, 500).</li> | <li>Contain fewer than the maximum number of genes. The maximum gene set size is set by the <span style="font-style: italic;">Max size </span>parameter (by default, 500).</li> | ||
| − | <li>Use the gene identifiers appropriate for this analysis:<br />If you are collapsing your dataset (<span style="font-style: italic;">Collapse dataset to gene symbols</span> parameter = True), the genes in the collapsed dataset are identified by gene symbol, so the gene identifiers in your gene sets must be gene symbols. <br />If you are not collapsing your dataset (<span style="font-style: italic;">Collapse dataset to gene symbols</span> parameter = False), the gene identifiers in your gene sets must be the same as those in your expression dataset.</li> | + | <li>Use the gene identifiers appropriate for this analysis:<br /> |
| + | If you are collapsing your dataset (<span style="font-style: italic;">Collapse dataset to gene symbols</span> parameter = True), the genes in the collapsed dataset are identified by gene symbol, so the gene identifiers in your gene sets must be gene symbols. <br /> | ||
| + | If you are not collapsing your dataset (<span style="font-style: italic;">Collapse dataset to gene symbols</span> parameter = False), the gene identifiers in your gene sets must be the same as those in your expression dataset.</li> | ||
</ol> | </ol> | ||
| − | <p>For more information about | + | <p>For more information about "appropriate" gene identifiers, see [http://www.broad.mit.edu/gsea/doc/GSEAUserGuideFrame.html?Consistent_Features Consistent Feature Identifiers Across Data Files] in the <em style="">GSEA User Guide.</em></p> |
| + | <p align="left"><strong>Illumina data</strong>: The probe identifiers for Illumina chips contain leading zeros. Certain programs, such as Excel, automatically remove leading zeros. If you are collapsing your dataset, the probe identifiers in your dataset must match the probe identifiers in the chip annotation file. If this error occurs and you are using Illumina data, check that the probe identifiers in your dataset include the leading zeros.</p> | ||
Latest revision as of 16:14, 15 February 2008
None of the gene sets that you specified passed the size threshold. Check that the selected gene sets:
- Contain more than the minimum number of genes. The minimum gene set size is set by the Min size parameter (by default, 15).
- Contain fewer than the maximum number of genes. The maximum gene set size is set by the Max size parameter (by default, 500).
- Use the gene identifiers appropriate for this analysis:
If you are collapsing your dataset (Collapse dataset to gene symbols parameter = True), the genes in the collapsed dataset are identified by gene symbol, so the gene identifiers in your gene sets must be gene symbols.
If you are not collapsing your dataset (Collapse dataset to gene symbols parameter = False), the gene identifiers in your gene sets must be the same as those in your expression dataset.
For more information about "appropriate" gene identifiers, see Consistent Feature Identifiers Across Data Files in the GSEA User Guide.
Illumina data: The probe identifiers for Illumina chips contain leading zeros. Certain programs, such as Excel, automatically remove leading zeros. If you are collapsing your dataset, the probe identifiers in your dataset must match the probe identifiers in the chip annotation file. If this error occurs and you are using Illumina data, check that the probe identifiers in your dataset include the leading zeros.
