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diff --git a/general/datasets/UMUTAffyExon_0209_RMA/processing.rtf b/general/datasets/UMUTAffyExon_0209_RMA/processing.rtf deleted file mode 100644 index 6e4dc8e..0000000 --- a/general/datasets/UMUTAffyExon_0209_RMA/processing.rtf +++ /dev/null @@ -1,9 +0,0 @@ -<p>The following steps were applied to refine the data by M. Jagalur in RWW lab:</p>
-
-<ol>
- <li>Strain correction: In this step the strong probe level cis-QTLs were identified and using an expectation maximization (EM)-like method, the genotypes of each marker was re-assigned. This set of reassigned markers was compared to existing list genotypes of BXD strains and the maximal match was identified as the correct strain.</li>
- <li>Sex correction: In this step probes that are highly correlated to sex were identified and using an EM-like method we detected and corrected the sex of single array data sets.</li>
- <li>Data exclusion criteria: In this step individual arrays were evaluated. Arrays were systematically excluded from the data set (drop one out) and the number of cis-QTLs was recomputed. If excluding an array resulted in s significantly higher number of cis-QTLs then that array was considered to be of poor quality and was excluded from the final data set This step was repeated across all arrays in multiple cycles until there was no improvement in number of cis-QTLs.</li>
- <li>Tissue correction: In this step probes that are highly correlated to tissue type were identified and EM-like method was used to identify correct tissue.</li>
- <li>Noise Removal: A noise component was calculated using the expression of "unhybridized"probes (those with the lowest signal) and was removed from the data.</li>
-</ol>
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