Figure 2.4.6 Reports menu. You may create either dynamic or tab-delimited text reports of either Samples or of subsets of genes.
These may be presented as interactive dynamic tables as well as scrollable text windows capable of being exported to Excel. If Web DB access is enabled, clicking on an entry will bring up a Web browser with access to GenBank data. If the report contains Clone ID as one of the fields, you can click on it to have it define that gene as the current gene and highlight it in the microarray image or scatter plot (if it is being used). The reports are divided into two types - those dealing with lists of arrays (i.e. the sample experimental condition) and those dealing with lists of genes.
The Report menu includes:
-
show tables of sample array information.
-
show tables of sets of genes information.
- generates the
table as 'Spreadsheet', 'Tab delimited', or 'Name=Value list'.
- changes
the report font size from default 10 point.
The "Samples vs Samples correlation coefficients" computes the correlation coefficients in an upper diagonal matrix for the current set of Filtered genes showing HP samples similarity. Then entries are of the following form where HP:1 and HP:2 correspond to samples listed in the field names of the table and the data is the intensity values using the current normalization method.
rSq=0.748, n=1656, HP:1(mn+-sd)=(28991+-19564), HP:2(mn+-sd)=(5044+-9766)
The "Calibration DNA summary" table contains the computed means, std-dev, and computed normalization scale factor for all active hybridized samples. The scale factors are used if the 'Calibration DNA' normalization is used.
You must set the Web access checkbox if you want to click on a blue hyperlink in the resulting report to access an associated Web database.
Figure 2.4.6.1 Hybridized samples dynamic Report windows. A) Samples Info report. B) Sample Web links. Clicking on a blue hypertext link brings up the corresponding genomic Web database entry in a separate Web browser window if the Web access is enabled. The tab-delimited version of the same reports (not shown) may be cut and then pasted into other programs such as an Excel spreadsheet. C) HP vs HP correlation table on genes passing the data Filter for all samples in the HP-=E list.
- show genes
that meet the data Filter criteria.
If Cy3/Cy5 ratio data is being analyzed, then the Highest (Lowest) F1/F2 entries become
Figure 2.4.6.2 Gene Report windows of 50 named genes with highest HP-X/HP-Y 'set' ratios. A) Dynamic gene report of 50 genes with highest HP-X/HP-Y 'set' ratios. A similar report may be generated for the lowest ratios or for single HP-X/HP-Y samples. This type of report may be generated for the highest or lowest Zdiff values when the Zscore normalizations are used. Clicking on a blue hypertext link brings up the corresponding genomic Web database entry in a separate Web browser window if the Web access is enabled. It also sets the current gene to the gene for that row. B) The tab-delimited version of the same report may be cut and then pasted into other programs such as an Excel spreadsheet.
Spreadsheet [RB] - some cells (indicated by blue) are
connected Web databases that are accessed by clicking on them (default).
Tab delimited - suitable for export [RB] - as in Excel, etc.
Set max # genes in highest/lowest report or filter [CB] -
sets the number of genes N to report or use in data Filter.
Add EP data to Gene-Reports [CB] - for each of the
samples in HP-E.
Use EP data in Gene-Reports [CB] - use raw EP data (under
the current normalization) else use data normalized to
0.0 to 1.0 by maximum value for all genes being displayed.
Add HP-X/-Y 'set' statistics data to Gene-Reports [CB] -
that includes (mean,stdDev,CV,n) for both the HP-X and
HP-Y sets.
12pt [RB]
10pt [RB] - (the default size)
8pt [RB]
