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We have developed pipelines to process and analyze tomato spotted array and Affymetrix array data,
respectively. For spotted array data, raw quantified array data
(data from image processing program such as Imagene and GenePix) were normalized using the
print-tip LOWESS normalization strategy. Poor quality spots (according to the flags from the image
processing program) and spots not expressed in both channels (empty spots, SiganlMean < (BckdMean +
(2 x BckdStdDev))) were filtered out. Spots with at least two replicated data points were included
in the downstream statistical analysis. False Discovery Rate (FDR; multi-test corrected p value) for
each gene was determined using the PaGE
(Patterns from Gene Expression) program with the maximum number of possible permutations. For Affymetrix array data, raw array data (CEL files) were normalized at the
probe level using the
gcRMA algorithm. The detection calls (present, marginal, absent) for each probe set were obtained
using the mas5calls function in the affy package. Only genes with at least one present call across all the compared samples
were used to identify differentially expressed genes. Significance of gene expression was determined
using the LIMMA package and raw p values of
multiple tests were corrected using False Discovery Rate.
We processed all the microarray data stored in the data warehouse
using the pipelines described above. All results can be downloaded from the
"Download" menu. We have also developed a set of interfaces and tools to efficiently explore the
analyzed array data, including tools to identify coexpression
of a given gene, to identify enriched GO terms
and altered metabolite pathways
in a given dataset, and to cluster expression profiles...
Note to TOM2 users: Due to the multiple printing formats of TOM2 arrays, the
system has stopped supporting the probe ID system for TOM2 arrays and started to use the original Plate IDs.
If you are using CGEP printed probe IDs, you can convert them to plate IDs
from here. Please contact us if your TOM2 arrays were printed elsewhere
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