Thanks for your answer Sébastien.
Hi used the Terms.tsv to do this. I extracted all my informations from all
the individual samples results and rebuild a file after.
However, the pattern that I'm talking about is the trend that the
categories for each samples seems to react the same. You don't find it
strange that all the categories in the middle of the graph seems to be
exactly the same, even the outlier points? It's like if there was some kind
of bias in the enrichments.
In the example that I sent you, I can clearly see that all those points at
0.12 for example are from the same sample.
Here are some of the data points :
For Sample EUR
Golgi_apparatus : 0.122954
endoplasmic_reticulum : 0.121175
tight_junction : 0.12086
For Sample RAN
Golgi_apparatus : 0.185641
endoplasmic_reticulum : 0.18288
tight_junction : 0.182007
What does this proportion column means anyway? For the RAN sample, this
column sum up to 116.054, while for Sample EUR, it's summing up to 79.25
for all the terms. Am I mixing to much things together by making a graph
from this?
Thanks a lot.
2013/12/18 Sébastien Boisvert <sebastien.boisver...@ulaval.ca>
> On 29/11/13 04:31 PM, JC Grenier wrote:
>
>> Hi Sebastion,
>>
>
> Hi,
>
>
>
>> I'm communicating directly with you cause I have a figure to show you
>> concerning some analysis that I'm doing with GO terms. I
>> looked into the different depth just to see if I can see some difference
>> between both groups that I'm working on and found some weird stuff.
>>
>>
> You should use Terms.tsv or Terms.xml because those for specific depths
> are not accurate because
> of mainly 2 reasons:
>
> 1. EMBL_CDS sequences are annotated with any GO term, not just with leaves
> in the GO classification
> 2. The GO classification is directed acyclic graph, but a GO term can have
> many parents.
>
> The depth files use recursive counts, whereas Terms.xml/Terms.tsv don't.
>
> In our paper, we used the most abundant terms from Terms.xml regardless of
> depth.
> ( http://genomebiology.com/2012/13/12/R122/figure/F5 )
>
> This was discussed before on https://github.com/sebhtml/ray/issues/158 and
> on http://permalink.gmane.org/gmane.science.biology.ray-
> genome-assembler/406
>
>
> P.S. the files for depths will likely be removed at some point. (see #
> 158).
>
>
> I took my results from the file Terms.tsv.
>>
>> Here's one example. Can you tell me why this pattern exists?
>>
>
> I don't understand what you expect me to see here.
>
> Perhaps it would be wise to draw 1 colored line per sample.
>
>
> Like all the dots aligned (first why are they aligned...?) are from the
>> same
>> sample? Is this a coverage or number of reads artifact?
>>
>
> The proportions are computed in terms of k-mer observations divided by
> total number of
> k-mer observations. So I don't think it is necessary to normalize here
> since they are
> relative numbers.
>
>
>> Thanks a lot for your help
>>
>> --
>> Jean-Christophe Grenier, M.Sc.
>>
>> -----------------------------------------
>> /Bio-informaticien/
>> /Laboratoire de Philip Awadalla/
>> /Laboratoire de Luis Barreiro/
>> /CHU Sainte-Justine/
>> //3175, Côte Sainte-Catherine, local B-607
>> ///Tél : 514-345-4931 poste 5199/
>> -----------------------------------------
>>
>
>
--
Jean-Christophe Grenier, M.Sc.
-----------------------------------------
*Bio-informaticien*
*Laboratoire de Philip Awadalla*
*Laboratoire de Luis Barreiro*
*CHU Sainte-Justine*
3175, Côte Sainte-Catherine, local B-607
*Tél : 514-345-4931 poste 5199*
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