Getting this error, while running local

[immuneAI]

Error in if (x <= 0) { : missing value where TRUE/FALSE needed

DF<-data.frame(SAMPLE=sample_names,MHC=MHC,EC=EC,SC=SC,CP=CP,AZ=AZ,IPS=IPS)
Error in data.frame(SAMPLE = sample_names, MHC = MHC, EC = EC, SC = SC, :
arguments imply differing number of rows: 79, 1, 0
write.table(DF,file="IPS.txt",row.names=FALSE, quote=FALSE,sep="\t")
Error in is.data.frame(x) : object 'DF' not found

Am I missing any genes?

[immuneAI]

Hey guys,

Here is the sample data.
test_sample.zip

[mui-icbi]

Dear venkataddala,

i just tried the test_sample.csv you provided and on the tcia website https://tcia.at/tools/tools/ipgTools and it works fine. i will have a look at the R code and i´ll let you know if there are some issues.

kind regards!

[immuneAI]

Thanks Mate, That's true it's working on website, but if i'm running locally it's' throwing the error.

[classycammy]

Dear venkataddala and MayerC-imed,

I am also facing the same issues. I am wondering if there any updates in this issue yet?

[mui-icbi]

It seems that the gene names you use in your dataset do not match with the genes in the IPS_genes.txt. We will update the list. Until it's updated, you can use the http://www.genenames.org/tools/all to check on the missing genes.

Best!

[thiagovidotto]

I am also having the same issue as venkataddala. I checked my dataset and it has all genes from IPS_genes list.

[immuneAI]

@thiagovidotto you can use this code to run locally, https://github.com/venkataddala/IPS_Recode

[thiagovidotto]

@venkataddala you are an angel! It worked perfectly. Thank you so much for your help!

[immuneAI]

@classycammy @thiagovidotto I found it's good to add sample_ID in the PDF generated as we work on huge sample number it's hard to see ID only on file name. So I made few more changes in code, get it here. https://github.com/venkataddala/IPS_Recode

[thiagovidotto]

@venkataddala I have used your code and it worked perfectly. However, as I use TCGA data, I was comparing the plots I generated for a tumor sample with the same sample at The Cancer Immunome Atlas (tcia.at). I observed that my results are divergent from the ones at TCIA. I wonder if I am doing something wrong or we might get something different from your code? What do you think? I am not an expert into this, so I couldn't spot the differences between the codes. Thanks!