Data not available about scprognosis HOT 7 CLOSED

Hi

@XiaomeiLi1 I am trying to use the scripts you wrote here but I have found many hardcoded parts and objects that is not available.

Would you mind if you upload or send me this data ?

load("/home/xiaomei/Topic1/data/TCGA753.rda")

Hi Aly,
Thank you for using our method. I can not upload data here because it is too big. I will upload it somewhere and share the link with you. And I can send you data as well.
Regards,
Xiaomei

from scprognosis.

Hi

@XiaomeiLi1 I am trying to use the scripts you wrote here but I have found many hardcoded parts and objects that is not available.

Would you mind if you upload or send me this data ?

load("/home/xiaomei/Topic1/data/TCGA753.rda")

Hi Aly,
Please download the data at the following link:

https://drive.google.com/file/d/184_yMMHc9KgDg7dHiA0hj639Vrs-iNs2/view?usp=sharing

Regards,
Xiaomei.

from scprognosis.

@XiaomeiLi1 Thanks a lot.
I will try to make a pull request with other things I found and fixed on my local repo (some missing libraries and some things related to preparing the data).

from scprognosis.

Hi @XiaomeiLi1 ,

I am still having some problems with missing data in benchdb.R file

  pd = survival_data[,c(5,7)] # os
  A = run_topN(mRNA = RNASeq_data, pd = pd, ranking = ranking) #RNASeq_data not found

  survival_data = pData(GEO)
  survival_data = pData(UK)
  survival_data = pData(METABRIC)

Would you mind if you check and send me those objects?

I highly appreciate your time.

Thanks,
Aly

from scprognosis.

Hi Aly,
Please download the datasets from the following links:
GSE114397: https://drive.google.com/file/d/1UEdLTsfAqiYuoIQ8pdASnbGfDe3H99Wv/view?usp=sharing

GEO: https://drive.google.com/file/d/1hNmetZgFLNRPL8JtT5UsJdEFUbLyThE5/view?usp=sharing

TCGA753: https://drive.google.com/file/d/184_yMMHc9KgDg7dHiA0hj639Vrs-iNs2/view?usp=sharing

UK: https://drive.google.com/file/d/1qBBh9KLhcn2OUpZfCtjuTOpefaMFbL6f/view?usp=sharing

For the METABRIC data, we cannot make it public because Metabric requires individual access agreement. However, you can go to the EMBL-EBI repository to apply for the data EGAS00000000083.

GSE114397, GEO, TCGA753, METABRIC, and UK are all the gene expression datasets used in this work. RNASeq_data is the gene expression data of TCGA753. If you load TCGA753 to your R Studio, you will see it.

I hope this can help you.
Thanks and regards,
Xiaomei.

from scprognosis.

Hi @XiaomeiLi1 ,

Thank you for your fast response. I am trying to access those files but the access is still private. I have sent you a request on all files on google drive and I am waiting for your reply.

Also, I found an issue related to this line in main file
vim.hr = vim.hr[,index]
I have received "Error in vim.hr[, index]: subscript out of bounds" . I tried to trace this problem but it seems related to generation of index

index = NULL for(i in 1:nrow(params1)) { index = c(index, which(apply(params, 1, function(x) all(params1[i,] == x)))) } length(index)

I don't understand why are you generating index in this way so I can fix it.

Would you mind if you take a look ?

Thanks,
Aly

from scprognosis.

Hi @XiaomeiLi1 ,

Thank you for your fast response. I am trying to access those files but the access is still private. I have sent you a request on all files on google drive and I am waiting for your reply.

Also, I found an issue related to this line in main file
vim.hr = vim.hr[,index]
I have received "Error in vim.hr[, index]: subscript out of bounds" . I tried to trace this problem but it seems related to generation of index

index = NULL for(i in 1:nrow(params1)) { index = c(index, which(apply(params, 1, function(x) all(params1[i,] == x)))) } length(index)

I don't understand why are you generating index in this way so I can fix it.

Would you mind if you take a look ?

Thanks,
Aly

Hi Aly,
I have approved the request. Please try it again. And you also can download these files from the public resources that I provided on the Readme file. Then you need to remove the ncRNA from the expression data.
The index is used for eliminating parameters are not satisfied with the constraint. I changed the code a bit to make it easy to understand.
Thanks and regards,
Xiaomei

from scprognosis.