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diff --git a/general/datasets/Inia_hyp_pca_0813_v2/processing.rtf b/general/datasets/Inia_hyp_pca_0813_v2/processing.rtf new file mode 100644 index 0000000..b3e8689 --- /dev/null +++ b/general/datasets/Inia_hyp_pca_0813_v2/processing.rtf @@ -0,0 +1 @@ +<p>Total RNA was processed using standard protocols and hybridized to the Affymetrix Mouse Gene 1.0 ST arrays4. This array contains 34,700 probe sets that target ∼29,000 well-deï¬ned transcripts (RefSeq mRNA isoforms). A single probe set is a collection of about 27 probes that target known exons within a single gene. The multiple probes design provides a more comprehensive cov-erage of transcripts from a single gene. Male and female samples were interleaved and processed together to avoid batch confounds. Details on the strain, age, and sex of each sample can be obtained from the information available for the INIA Hypothalamus Affy MoGene 1.0 ST (Nov10) data set on www.genenetwork.org. Probe set level intensity values were extracted from the CEL ï¬les using the Affymetrix GeneChip Operating Software. Data nor-malization was performed using the R package “Affy” available from www.Bioconductor.org. The Robust Multichip Averaging protocol was used to process the expression values. The array data was then log transformed and rescaled using a z-scoring procedure to set the mean of each sample at eight expression units with a SD of 2 units. The entire data set can be down-loaded from www.genenetwork.org using the accession number GN281 (http://www.genenetwork.org/webqtl/main.py?FormID = sharinginfo&GN_AccessionId = 281) and also from the NIH Gene Expression Omnibus5 using the GEO accession number GSE36674. For this study we used a subset of cases that were repre-sented by both male and female samples – 78 sex-balanced arrays. Statistical power provided by this sample size (N = 39 strains) was estimated using the R function power.t.test6 with the SD set at 0.17, which is the average value. Only transcripts with above aver-age expression (minimum expression value above 8.5 on a log2 scale) were included for further analysis (17,192 probe sets). We used a two-tailed paired t -test to identify transcripts with signiï¬-cant expression difference between males and females. We applied the Benjamini and Hochberg false discovery rate (FDR) method and selected differentially expressed transcripts using a 10% FDR criterion.</p>
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