Issue with blood Tissue

[iramiller5151]

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]

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.