Susanc and noys FAQ
Regardless of the application applied, after hybridization and washes, Affymetrix arrays are scanned by the Affymetrix scanner. The output of the scan is a CEL file which is the "raw data" and is the input for most downstream analysis software. Although you might not be able to open this file, CEL file is your raw data and it is crucial to save it.
For Expression arrays, the unit runs the "Expression Console" software, which quantifies, normalizes and gives some QC measures of the arrays. We also do some QC on "Partek". Consequently, you will receive output files of these software, namely:
- A "pivot" table, which is the quantified (and normalized) data, in text format, which can be opened in Excel. Each row is a probe-set, while each column is a sample (i.e. an array), and the figure is the signal intensity. The algorithm used is RMA for ST arrays and MAS5 for 3-prime arrays. Updated annotations of the probe-sets are attached to the table (last column).
- A "full_report" with QC measures of the array, in text format which can be opened in Excel. Measures out-of-spec will be labeled in orange
- A pdf file with QC images including: a signal histogram of all arrays in the experiment, a Box-Plot of the signal distribution; Pearson Correlation of all samples, Line graphs of PolyA and Hyb controls.
- PCA and Hierarchical Clustering of the arrays in the experiment.
You will also receive a "sample" Excel file, which is a conversion table between the name you gave your sample and the code it received by the unit for processing.
Detailed information about SNP array output files can be found here (*link to file)
Regardless of the application applied, after hybridization and washes, Agilent arrays are scanned by the Agilent scanner. The output of the scan is a TIFF file. Whether running a single- or a dual-dye hybridization, a single file is generated. This file is the "raw data" and is the input for most downstream analysis software. For all types of Agilent arrays, the unit runs the "Feature Extraction" software, which quantifies, normalizes and gives some QC measures. You will receive output files of this software, namely:
- A tabulated text file, which is the quantified (and normalized) data. Each array has a separate file, in which each row is a probe (i.e. spot).
- A jpeg image of each array
- A pdf with a QC report
You will also receive a "sample" Excel file, which is a conversion table between the name you gave your sample and the code it received by the unit for processing, as well as which sample/s were placed on each array.
You will receive by email a pdf file with the results of your analyzed samples. One file is generated for each "chip" carrying up to 12 (nano) or 11 (pico) samples. For each sample you will have a graph, a table and a calculated gel image. Intactness of sample is represented by the RIN (=RNA Integrity Number). 10 is the maximum, and the higher the number the higher the integrity. Respectively 2 distinct and sharp peaks (on graph) or bands (on gel image) should appear representing the 18S and 28S.