[Genome] The GNF tables

[Yael Altuvia]

Hi,


I have a few questions regarding the GNF tables.


A. I tried to reconstruct the normalization procedure leading to the 
values of the gnfAtlas2 table from the raw data

in  gnfHumanAtlas2All  (I used the hg17 and hg17 fixed)


I conducted the following:


1. conversion between the indexing of the 158 two sample entries to the 
79 entries

    For that I used the gnfHumanAtlas2AllExps and the 
gnfHumanAtlas2MedianExps

    I compared them by their names. Most were identical but two differed

    1. pituitary v. pituitary gland
    2. DRG v. dorsal root gangelion 

    I assumed they are the same sample


    I also used this files to assign the group to each tissue (e.g. 
brain immune etc)


2. For each sample of the 158 samples in "all" I calculated the median 
of each group


3.  I run into some problems trying to calculate the log ratio of each 
entry. According to the previously asked questions relating to this 
topic I calculated the log ratio of each entry by dividing it by the 
median of its group. but the values I got differed from the gnfAtlas2.  
I also tried to use instead the median of the group medians for the 
normalization? (this gives more similar values although they still seem 
to differ)  (in both cases I calculated the median of the two samples 
after applying the procedure). What am I doing wrong?

 

B. Regarding the gnfAtlas2Distance I would like to know
    a. what is the function used for the vector comparisons?
    b. what "_at" are related to each gene (all the exonic _at's?,  a 
representative _at?)


Thanks for your help

Yael Altuvia










5. the distance what function between them and according to what 
assignment (the best the exons etc..)