search

lanagarmire / Asgard

Other
37 stars 15 forks source link

Issue with blood Tissue #6

Open iramiller5151 opened 1 year ago

iramiller5151 commented 1 year ago

Hi,

Thanks for all the work on this tool. I am having trouble getting results for the blood tissue (I did loaded the specific tissue related drugs). I tried a few other tissue types including breast, kidney, lymphatic tissue and they seemed to work fine but for some reason the blood keeps throwing this error.

error

"reading /Users/iradm/Asgard/GSE92742_Broad_LINCS_Level5_COMPZ.MODZ_n473647x12328.gctx done reading /Users/iradm/Asgard/GSE70138_Broad_LINCS_Level5_COMPZ_n118050x12328.gctx Error in process_ids(cid, all_cid, type = "cid") : none of the requested cid were found in the dataset"

My code is below

read in specific tissue related drugs as previously created

my_gene_info<-read.table(file="/Users/iradm/Asgard/DrugReference/blood_gene_info.txt",sep="\t",header = T,quote = "") my_drug_info<-read.table(file="/Users/iradm/Asgard/DrugReference/blood_drug_info.txt",sep="\t",header = T,quote = "") drug.ref.profiles = GetDrugRef(drug.response.path = '/Users/iradm/Asgard/DrugReference/blood_rankMatrix.txt', probe.to.genes = my_gene_info, drug.info = my_drug_info)

Repurpose mono-drugs for every cell type

Drug.ident.res = GetDrug(gene.data = Gene.list, drug.ref.profiles = drug.ref.profiles, repurposing.unit = "drug", connectivity = "negative", drug.type = "FDA")

GSE92742.gctx.path="/Users/iradm/Asgard/GSE92742_Broad_LINCS_Level5_COMPZ.MODZ_n473647x12328.gctx" GSE70138.gctx.path="/Users/iradm/Asgard/GSE70138_Broad_LINCS_Level5_COMPZ_n118050x12328.gctx" Tissue = "blood"

ds <- parse.gctx(GSE70138.gctx.path)

Drug.score<-DrugScore(SC.integrated=SC.integrated, Gene.data=Gene.list, Cell.type=NULL, Drug.data=Drug.ident.res, FDA.drug.only=TRUE, Case=Case, Tissue= Tissue, GSE92742.gctx=GSE92742.gctx.path, GSE70138.gctx=GSE70138.gctx.path)

Any ideas?

hebinghb commented 1 year ago

How about using "haematopoietic and lymphoid tissue" instead of "blood"? There is only one cell line U266 under "blood" in L1000 data. It's in GSE92742 but not in GSE70138. That's why it reported an error.