Error occured in "calculate_single"

[ACS0906]

I am trying to run your example.R commands but shows error just like bellow.

results<- calculate_single(data, condition, binSize=0.2,nperm=5) do EMD for Hur genes. Calculating pairwise emd scores....................Error in file(con, "w") : cannot open the connection

Any suggestion..???

[tianyu-github]

I have never seen this error before, could you provide more details about the error? What is the RStudio version are you using? Could you try to run function file SigEMDHur.R and SigEMDnonHur.R in your console, then run the example?

[79176609]

According to your suggestions, I'm tried but failed. After running SigEMDHur.R and SigEMDnonHur.R files in R (version: R.3.4.3) for example.R, I get the error like....

results<- calculate_single(data, condition, binSize=0.2,nperm=100) do EMD for Hur genes. Calculating pairwise emd scores...Error: BiocParallel errors element index: 1, 2, 3, 4, 5, 6, ... first error: could not find function ".emd_gene_pairwise"

Sorry for tardy reply.

Thanks in advance

[tianyu-github]

Hi, I've updated the code. Now you can try agian. Let me know if there are still errors.

[79176609]

Yeah..! It is working

Thanks again

[ACS0906]

Dear Mr. Tianyu,

Could you tell me why your method needed TPM normalized data instead of other normalization? I ask you because of the DE genes after TPM normalization is seemed misleading. Thanks in advance.! Kind regards, Singha Atul Chandra

[tianyu-github]

Hi,

We did not include a normalization in this tool, so we need normalized expression values as input. Actually, any kind of normalization can be used to this method, not only log-transformed TPM value.

[ACS0906]

Ok, Thank you. I see.

[adminshuang]

I have run the example.R perfectly well.But while I try my own data with the instruction: results<- calculate_single(data = data,condition = condition,Hur_gene = Hur_gene, binSize=0.2,nperm=100) it always gives the terrified error as below: do EMD for Hur genes. Calculating pairwise emd scores...Error in seq.default(floor(min(c(dataA, dataB))), ceiling(max(c(dataA, : 'from' must be a finite number I get little confused with the intrinsic code logic.What is wrong with my instruction??

[tianyu-github]

I think the reason is your data has some rows (genes) that are zeros among all the columns. You may try to remove those genes to clean up the data. I may include a function in the code to clean up data in the future.

[tianyu-github]

I've updated the codes and added a function "dataclean", you may want to have a try. Let me know if you still have errors.

On Thu, Mar 21, 2019 at 6:07 AM TOWARDSzs notifications@github.com wrote:

I have run the example.R perfectly well.But while I try my own data with the instruction: results<- calculate_single(data = data,condition = condition,Hur_gene = Hur_gene, binSize=0.2,nperm=100) it always gives the terrified error as below: do EMD for Hur genes. Calculating pairwise emd scores...Error in seq.default(floor(min(c(dataA, dataB))), ceiling(max(c(dataA, : 'from' must be a finite number I get little confused with the intrinsic code logic.What is wrong with my instruction??

— You are receiving this because you commented. Reply to this email directly, view it on GitHub https://nam01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgithub.com%2FNabaviLab%2FSigEMD%2Fissues%2F1%23issuecomment-475172145&data=02%7C01%7Ctianyu.wang%40uconn.edu%7Ce752629449c0413cc47108d6ade51354%7C17f1a87e2a254eaab9df9d439034b080%7C0%7C0%7C636887596730852997&sdata=kBxJKwNrLoMKADntMR3We3k7yKQbtPZek4Bdtjsac9Y%3D&reserved=0, or mute the thread https://nam01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgithub.com%2Fnotifications%2Funsubscribe-auth%2FAUVKI4RTBIQcHOmcDhertlPMEO-CcvX2ks5vY1n0gaJpZM4RpI6P&data=02%7C01%7Ctianyu.wang%40uconn.edu%7Ce752629449c0413cc47108d6ade51354%7C17f1a87e2a254eaab9df9d439034b080%7C0%7C0%7C636887596730863001&sdata=6YU21wRyotib21Qo459rVY%2Bs2yzoan6RlZWFwp6Gmuc%3D&reserved=0 .

[adminshuang]

I've updated the codes and added a function "dataclean", you may want to have a try. Let me know if you still have errors. … On Thu, Mar 21, 2019 at 6:07 AM TOWARDSzs @.***> wrote: I have run the example.R perfectly well.But while I try my own data with the instruction: results<- calculate_single(data = data,condition = condition,Hur_gene = Hur_gene, binSize=0.2,nperm=100) it always gives the terrified error as below: do EMD for Hur genes. Calculating pairwise emd scores...Error in seq.default(floor(min(c(dataA, dataB))), ceiling(max(c(dataA, : 'from' must be a finite number I get little confused with the intrinsic code logic.What is wrong with my instruction?? — You are receiving this because you commented. Reply to this email directly, view it on GitHub https://nam01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgithub.com%2FNabaviLab%2FSigEMD%2Fissues%2F1%23issuecomment-475172145&data=02%7C01%7Ctianyu.wang%40uconn.edu%7Ce752629449c0413cc47108d6ade51354%7C17f1a87e2a254eaab9df9d439034b080%7C0%7C0%7C636887596730852997&sdata=kBxJKwNrLoMKADntMR3We3k7yKQbtPZek4Bdtjsac9Y%3D&reserved=0, or mute the thread https://nam01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgithub.com%2Fnotifications%2Funsubscribe-auth%2FAUVKI4RTBIQcHOmcDhertlPMEO-CcvX2ks5vY1n0gaJpZM4RpI6P&data=02%7C01%7Ctianyu.wang%40uconn.edu%7Ce752629449c0413cc47108d6ade51354%7C17f1a87e2a254eaab9df9d439034b080%7C0%7C0%7C636887596730863001&sdata=6YU21wRyotib21Qo459rVY%2Bs2yzoan6RlZWFwp6Gmuc%3D&reserved=0 .

Well, thanks to your quickly reply. But the solution doesn't solved the problem. I applied my data to the new update version, it doesn't work.......And I checked the genes, it was filtered 0 out before. What a shame! It seems to have another reason. I will try to find out. The error recall I got still like this :

Calculating pairwise emd scores...Error in seq.default(floor(min(c(dataA, dataB))), ceiling(max(c(dataA, : 'from' must be a finite number Calls: calculate_single ... tryCatch -> tryCatchList -> tryCatchOne -> In addition: Warning messages: 1: In min(c(dataA, dataB)) : no non-missing arguments to min; returning Inf 2: In max(c(dataA, dataB)) : no non-missing arguments to max; returning -Inf Execution halted

[tianyu-github]

I've updated the codes and added a function "dataclean", you may want to have a try. Let me know if you still have errors. … On Thu, Mar 21, 2019 at 6:07 AM TOWARDSzs @.***> wrote: I have run the example.R perfectly well.But while I try my own data with the instruction: results<- calculate_single(data = data,condition = condition,Hur_gene = Hur_gene, binSize=0.2,nperm=100) it always gives the terrified error as below: do EMD for Hur genes. Calculating pairwise emd scores...Error in seq.default(floor(min(c(dataA, dataB))), ceiling(max(c(dataA, : 'from' must be a finite number I get little confused with the intrinsic code logic.What is wrong with my instruction?? — You are receiving this because you commented. Reply to this email directly, view it on GitHub https://nam01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgithub.com%2FNabaviLab%2FSigEMD%2Fissues%2F1%23issuecomment-475172145&data=02%7C01%7Ctianyu.wang%40uconn.edu%7Ce752629449c0413cc47108d6ade51354%7C17f1a87e2a254eaab9df9d439034b080%7C0%7C0%7C636887596730852997&sdata=kBxJKwNrLoMKADntMR3We3k7yKQbtPZek4Bdtjsac9Y%3D&reserved=0, or mute the thread https://nam01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgithub.com%2Fnotifications%2Funsubscribe-auth%2FAUVKI4RTBIQcHOmcDhertlPMEO-CcvX2ks5vY1n0gaJpZM4RpI6P&data=02%7C01%7Ctianyu.wang%40uconn.edu%7Ce752629449c0413cc47108d6ade51354%7C17f1a87e2a254eaab9df9d439034b080%7C0%7C0%7C636887596730863001&sdata=6YU21wRyotib21Qo459rVY%2Bs2yzoan6RlZWFwp6Gmuc%3D&reserved=0 .

Well, thanks to your quickly reply. But the solution doesn't solved the problem. I applied my data to the new update version, it doesn't work.......And I checked the genes, it was filtered 0 out before. What a shame! It seems to have another reason. I will try to find out. The error recall I got still like this :

Calculating pairwise emd scores...Error in seq.default(floor(min(c(dataA, dataB))), ceiling(max(c(dataA, : 'from' must be a finite number Calls: calculate_single ... tryCatch -> tryCatchList -> tryCatchOne -> In addition: Warning messages: 1: In min(c(dataA, dataB)) : no non-missing arguments to min; returning Inf 2: In max(c(dataA, dataB)) : no non-missing arguments to max; returning -Inf Execution halted

Hi, The error occurred because function (min(x)) where x is a numeric(0) which means x is nothing. Could you check your variable "condition"? Set names for "condition", you could add "names(condition) <- colnames(data)" right after generating the vectors for "condition". Please let me know if it works or not.

[adminshuang]

Yeah,that's the problem,The solution solved my problem perfectly!!Thanks a lot.