The tissueenrich's discuss from tuteja-lab

tissueenrich's Issues

TSGE vs. TWAS

Hi,

Can I ask what is the foundamental difference between tissue-specific gene enrichment and TWAS (http://gusevlab.org/projects/fusion/)?

Thanks!

best regards,
Jie HUANG, MD MPH PhD

The tissue specific genes in database

I found although many genes are identified as tissue-specific in my list, there is no significant P-value. I guess the number of tissue-specific genes in that category is very large. But is there any way I can check the number or the genes in each tissue-specific genes category? Thanks!

"Missing value where true/false needed" error with teGeneRetrieval

Hi Ashish,

I'm trying to create a custom TissueEnrich dataset but having an issue with the teGeneRetrieval. Specifically, my commands are:

> head(test[,1:7])
                  CTBs        EPI       EVTs   Hypoblast        ICM    PSA.EPI       STBs
A4GALT       28.256089  87.818451   9.739999  35.0449376 124.365134 14.0052407  3.8816029
AAAS        166.393659 176.695678 169.025785 166.5609337 178.972602 54.4752599 73.8415541
AACS          3.705388  10.217619   8.844224  11.4724415   5.290590  4.9312505  3.2401403
AADACL2      13.170123   2.072885  16.220174   0.5474843   2.843561  3.5183490 18.3895300
AADACL2-AS1   9.378275   3.074869   8.883682   0.6346828   3.913311  4.3598354 11.7280428
AADACL3       3.670026   5.607436  26.660207  36.3240296   5.195383  0.4045552  0.2788972
> test <- test[,1:7]
> se<-SummarizedExperiment(assays = SimpleList(as.matrix(test)),rowData = row.names(test),colData = colnames(test))
> te.dataset.xiang <-teGeneRetrieval(se)
Error in if (sum(idx) > 0) { : missing value where TRUE/FALSE needed

Could you please help me fix this?

Thanks!

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