[BioC] Problems with golubEsets dataset
cinderole at sina.com
Sun Oct 26 08:54:13 MET 2003
When I begin to analysis the golubEsets dataset and make a simple pre-processing step,I find a strange phenomena.
The pre-processing steps follows the suggestion of S. Dudoit et al.(2002, JASA,personal communication with Pablo Tamayo):(1) thresholding: floor of 100 and ceiling of 16000; (ii) filetering: exclusion of genes with max/min<=5 and (max-min)<=500, where max and min refer respectively to the maximum and minimum expression levels of a particular gene across mRNA samples;(iii) base 10 logarithmic transformation.
If only pre-processing with thresholding,the dataset are summarized by a 7129*72 matrix, where there are 4260(0.784%) with values 16000,242087(47.164%) with values 100, totally 47.948%.
If pre-processing with thresholding & filtering, the dataset are summarized by a 3571*72 matrix, where there are 987(0.384%) with values 16000, 50321(19.572%) with values 100, totally 19.956%.
I wonder whether we can get some interesting expression pattern from such noisy dataset. I have written to the original author of the datasets,but unfortunately he cann't give me a good reason. I write this letter to the Bioconductor list to see if someone could give me a explanation.
Waiting for reply!
¡¡¡¡¡¡¡¡¡¡¡¡¡¡¡¡cinderole at sina.com
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