Help with interpreting GEO derived data values
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@ochsner-scott-a-4334
Last seen 7.4 years ago
Hi, I've imported a GSE object using; > gse<-getGEO("GSE444") >gse<-gse$$GSE444_series_matrix.txt.gz > class(gse) [1] "ExpressionSet" attr(,"package") [1] "Biobase" The data look like: > head(exprs(gse)) GSM6778 GSM6779 GSM6780 GSM6781 GSM6782 GSM6783 GSM6784 GSM6785 GSM6786 GSM6787 1000_at 10763.1 12469.0 9200.9 8988.6 8021.9 13376.4 9657.0 9835.3 10779.6 8374.2 1001_at 721.7 1538.3 827.9 1123.3 828.3 1699.9 864.9 989.2 940.2 1012.0 1002_f_at 606.4 285.9 364.1 651.4 347.2 794.6 770.5 573.1 1239.8 1324.0 1003_s_at -687.9 -3701.3 -1040.8 -754.0 -748.6 -671.6 -1103.8 -1509.7 -769.9 -4944.8 1004_at 1224.6 -714.3 690.4 1130.4 780.9 1002.9 2096.1 594.1 773.2 813.7 1005_at -119.7 -408.7 93.9 182.3 -209.3 705.0 -178.7 394.1 -161.2 -910.4 Now the above values don't' look normalized. From the GSE444 summary I read, "The raw data are presented. The computations in the manuscript were based on the fold-changes reported by the MAS 4.0 software, not on ratios taken from raw data." It appears that the investigators have provided some sort of raw data, presumably the MAS4.0 pm values, and not a processed and normalized expression value. I would have used the .CEL files if the authors had bothered to deposit them. I would greatly appreciate it if anyone could help shed some light on the nature of the above values and how to go about normalizing them. Regards, Scott > sessionInfo() R version 2.13.0 (2011-04-13) Platform: i386-pc-mingw32/i386 (32-bit) locale: [1] LC_COLLATE=English_United States.1252 LC_CTYPE=English_United States.1252 LC_MONETARY=English_United States.1252 LC_NUMERIC=C [5] LC_TIME=English_United States.1252 attached base packages: [1] tools stats graphics grDevices utils datasets methods base other attached packages: [1] GEOquery_2.19.2 hgu95av2.db_2.5.0 org.Hs.eg.db_2.5.0 RSQLite_0.9-4 DBI_0.2-5 AnnotationDbi_1.14.1 limma_3.8.2 affy_1.30.0 [9] Biobase_2.12.2 loaded via a namespace (and not attached): [1] affyio_1.20.0 preprocessCore_1.14.0 RCurl_1.6-6.1 XML_3.4-0.2 Scott A. Ochsner, PhD Baylor College of Medicine One Baylor Plaza Mail Stop: BCM-130 Houston, TX 77030 Voice: (713) 798-6227 Fax: (713) 790-1275
GO hgu95av2 GO hgu95av2 • 611 views
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