Mixed cell-type samples deconvolution from expression data + tumor applications

[Kevin Rue]

Hi all,

As we discussed applications of mixed tissue deconvolution to other similar types of experiments, I found this mention of tumor-purity estimation that we mentioned with Yue Fan in this paper (http://www.ncbi.nlm.nih.gov/pubmed/24148234) by the same author who developed the R package I presented (CellMix). Have a look at table 1 for suggested applications of the approach.

As we mentioned we Brendan too, I believe the same approach (if not the same package) could be applied to the identification of bacterial proportions in different activation states. Anything is worth trying really, as long as a set of pure samples are available for each cell type/tissue considered.

How accurate this approach is in each case remains to be evaluated in each separate case with an adequate validation set (at least, that is my opinion). 

I am still in the process of evaluating the conversion of a human cell blood count signature to bovine samples.

Regarding upcoming meetings, I suggest:

• Date
• 9th December, 2pm, Interactive Hub
• Possible topics:
• Introduction to E.coli genome assembly, by Lisa Rogers (TBC)
• ...feel free to add more here and reply this email !

Regards,

Kevin

--
Kévin RUE-ALBRECHT
Computational Infection Biology PhD Programme
University College Dublin
Ireland
http://fr.linkedin.com/pub/k%C3%A9vin-rue/28/a45/149/en

[Lisa Rogers]

Hi,

I didn't get a chance to put some slides together and I won't get a chance to this morning, so I'd like to postpone talking about contig assembly this week. 

Thanks,

Lisa

[Kevin Rue]

Hi all,

Sorry for the late notice, but let me confirm that today's meeting is cancelled.

• Now, I am not sure how many people would like to meet next week (16th) for a pre-Christmas meeting.
  
• If no answer, I guess we can schedule the meetings to resume on Monday January 13th.
  

Regards

Kevin

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