Biology Reference
In-Depth Information
filtering the gene expression profile to eliminate those that do not
satisfy some simple criteria; and
standardizing or rescaling the profiles to generate vectors of length one.
Mouse 430 v2 Affymetrix GeneChip arrays are used for all experi-
ments. Probe intensity data as CEL files are imported into the R software
environment (http://www.R-project.org). Probe-level data quality is
assessed using image reconstruction, histograms of raw signal intensities,
and MA plots. Normalization is performed for each batch separately using
the RMA (affy/RMA; http://www.bioconductor.org) method, using all
probe intensity data sets together to form one expression measure per
probe set per array.
Fold change analysis is conducted for each pair of comparisons as listed
above. The results are summarized in two sets of files. The first file lists
fold change for every probe set on the microarray; the second file lists fold
change of
2 or more. Once opened in Microsoft Excel and sorted by the
column of fold change in descending order, the probes that showed the
largest fold changes will present at the top and the bottom of the sorted list.
In these files, the first four column names are as follows (from left to
right):
±
Clone id
name of the gene probes
Log2 ( rma.expr_P190 )
=
=
log 2 -transformed RMA-processed
expression for P190
Log2 ( rma.expr_P210 )
log 2 -transformed RMA-processed
expression for P210
Relative.fold.change_P190.relative.to.P210
=
=
2 ^ absolute.value.of (Log2(rma.expr_P190)
Log2(rma.expr_P210))
=
expression ratio of P190 vs. P210.
For example, probe 1455238_at has a relative fold change of 19.50; this
means that it is upregulated in P190 compared with P210, and that P190
is 19.50 times higher than P210. On the other hand, probe 1450140_a_at
has a relative fold change of
7.605; this means that it is downregulated
in P190 compared with P210, and that P210 is 7.6 times higher than P190.
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