zhandong / dsa

Digital Sorting Algorithm

DSA

Digital Sorting Algorithm

Background Cellular heterogeneity is present in almost all gene expression profiles. However, transcriptome analysis of tissue specimens often ignores the cellular heterogeneity present in these samples. Standard deconvolution algorithms require prior knowledge of the cell type frequencies within a tissue or their in vitro expression profiles. Furthermore, these algorithms tend to report biased estimations.

Results Here, we describe a Digital Sorting Algorithm (DSA) for extracting cell-type specific gene expression profiles from mixed tissue samples that is unbiased and does not require prior knowledge of cell type frequencies.

Conclusions The results suggest that DSA is a specific and sensitivity algorithm in gene expression profile deconvolution and will be useful in studying individual cell types of complex tissues.

dsa's Issues

estimated weight/proportion greater than 1 for a specific cell type

Dear the owner: When applying the DSA algorithm to my microarray data of RNA expression from nasopharygnx (NP) specimens that contains two major cell types: epithelial and blood/immune cells, I got the estimated weight/proportion for epithelial cells greater than 1 in several of the 26 NP samples (see attached file). Is this normal? Should I re-scale the 2 weights (epithelial and blood) for a sample to a sum of 1 (100%)? I tried the re-scale, and the overall estimates across 4 groups of samples looked very close to the reality biologically, i.e. that more infection, the less epithelial cells in the epithelial-blood mixed samples. I am here with the hope to get an expert opinion on how to deal with this issue with the DSA package. Thank you!
estimated_weight_QLM_157markers.xlsx

Trouble installing DSA package

Using both R studio & R x64 3.1.1
Package not recognised in appropriate directory on computer where I placed it (i.e. not available to be selected). Have done this for other packages in the past with no problems. Am I missing something here?
Many thanks for your help

Archieve is broken

It looks like .tar.gz file is broken.
Anyway it would be better to put here unpacked source files.