User Guide

Uploading Data
Using QuickLoad Wizard
Affymetrix Manual Column Detection
The Upload Wizard will automatically detect
the proper data columns for text files
generated from MAS 4, MAS 5 and GCOS. If
auto detection fails, you can use Manual
Column Detection.
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1. Affymetrix MAS 5 data format. This is
an example of a file from the U34B
GeneChip®. Formats may vary due to
differences in export from MAS 5.
Generally the first column will contain
the probeset ID. This identifies each
gene on the array. The two columns
that are needed by GeneSifter for
analysis are the columns containing the
signal and detection value for that
probe set. In this example, column B,
which is labeled Signal, contains the
derived signal value and column C,
labeled Detection, contains the quality
value. There may be additional
columns present in a data file and the
heading for the signal and quality
values may be different than what is
presented here. In general the signal
column will either be labeled Signal or
will have the word Signal at the end of
the column name. This column can
contain both positive and negative
numbers. The quality column will
generally be labeled Detection or will
have the word Detection at the end of
the name. This column will contain the
letters A, M and P.