NITUMID top level function

[lzy604]

Hi,

Thanks for developing this tools. When I use the function"NITUMID" ,I got this warning message. And the out file is all NA. Could you help me to solve this problem? Thanks!

Warning message: In rnorm(dim(Y_scale)[1] dim(Y_scale)[2], 0, 0.1 sd(Y_scale)) : NAs produced

[tdw1221]

Hi, could you check:

  1)  if there are NA entries in your input gene expression matrix Y
  2)  if there are rows/columns of 0s in your input gene expression matrix Y

Thanks

[lzy604]

Hi, could you check:

  1)  if there are NA entries in your input gene expression matrix Y
  2)  if there are rows/columns of 0s in your input gene expression matrix Y

Thanks

Hi,

Thanks for your reply! I have checked the matrix as your suggestions. There is no NA in the matrix, but there are lots of 0s in the matrix. Do you mean the method does not support the gene with no expression or not detectable？Maybe I need to change the 0s as 0.00001?

Thanks, Ziyi

[tdw1221]

You can have 0s in your data matrix, but you are not supposed to have entire rows/columns of 0s.

If you don't mind, you can send me a sample of your data matrix and I could take a look at it.

nuan604 notifications@github.com 于2019年11月20日周三 下午9:50写道：

Hi, could you check:

1) if there are NA entries in your input gene expression matrix Y

2) if there are rows/columns of 0s in your input gene expression matrix Y

Thanks

Hi,

Thanks for your reply! I have checked the matrix as your suggestions. There is no NA in the matrix, but there are lots of 0s in the matrix. Do you mean the method does not support the gene with no expression or not detectable？Maybe I need to change the 0s as 0.00001?

Thanks, Ziyi

— You are receiving this because you commented. Reply to this email directly, view it on GitHub https://github.com/tdw1221/NITUMID/issues/1?email_source=notifications&email_token=ADX7LO767DFJX7B567N3ADDQUXZRDA5CNFSM4JPNNVIKYY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOEEYURUY#issuecomment-556878035, or unsubscribe https://github.com/notifications/unsubscribe-auth/ADX7LO7YLJDISZHXM2TOHO3QUXZRDANCNFSM4JPNNVIA .

[lzy604]

Hi,

Thanks so much for your help! I attached the matrix for you.

By the way, the input matrix should be TPM, log2 TPM or read counts? ST_mel1_rep1_log2tpm.txt

[tdw1221]

Sorry for the late reply, I will look into your data now and get back to you ASAP.

thanks

nuan604 notifications@github.com 于2019年11月22日周五 上午1:50写道：

Hi,

Thanks so much for your help! I attached the matrix for you.

By the way, the input matrix should be TPM, log2 TPM or read counts? ST_mel1_rep1_log2tpm.txt https://github.com/tdw1221/NITUMID/files/3878261/ST_mel1_rep1_log2tpm.txt

— You are receiving this because you commented. Reply to this email directly, view it on GitHub https://github.com/tdw1221/NITUMID/issues/1?email_source=notifications&email_token=ADX7LO3OL4A2CW4CRERVTE3QU56JRA5CNFSM4JPNNVIKYY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOEE4XKBI#issuecomment-557413637, or unsubscribe https://github.com/notifications/unsubscribe-auth/ADX7LOYP7PQYPO7PZME7Z53QU56JRANCNFSM4JPNNVIA .

[lzy604]

Thanks! Looking forward to your reply.

Thanks, Ziyi Li

Computational Cancer Genomics Lab School of Life Science and Technology Tongji University Shanghai, China

tdw1221 notifications@github.com 于2019年11月27日周三 上午6:04写道：

Sorry for the late reply, I will look into your data now and get back to you ASAP.

thanks

nuan604 notifications@github.com 于2019年11月22日周五 上午1:50写道：

Hi,

Thanks so much for your help! I attached the matrix for you.

By the way, the input matrix should be TPM, log2 TPM or read counts? ST_mel1_rep1_log2tpm.txt < https://github.com/tdw1221/NITUMID/files/3878261/ST_mel1_rep1_log2tpm.txt>

— You are receiving this because you commented. Reply to this email directly, view it on GitHub < https://github.com/tdw1221/NITUMID/issues/1?email_source=notifications&email_token=ADX7LO3OL4A2CW4CRERVTE3QU56JRA5CNFSM4JPNNVIKYY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOEE4XKBI#issuecomment-557413637 , or unsubscribe < https://github.com/notifications/unsubscribe-auth/ADX7LOYP7PQYPO7PZME7Z53QU56JRANCNFSM4JPNNVIA

.

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub https://github.com/tdw1221/NITUMID/issues/1?email_source=notifications&email_token=AJKOJ76UGHUHIT5FX6VSJXDQVWMN5A5CNFSM4JPNNVIKYY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOEFHS3FQ#issuecomment-558837142, or unsubscribe https://github.com/notifications/unsubscribe-auth/AJKOJ7YLJMS45FSYIEEGYZ3QVWMN5ANCNFSM4JPNNVIA .

[tdw1221]

Hi,

I look into your dataset, from the scale of the dataset it looks like

you are using a log2 transformed data. However, for deconvolution method to work, you need to transform them back to raw scale. I have attached example code I use to run NITUMID on your data, and it did not produce any error on my side.

hope it helps

nuan604 notifications@github.com 于2019年11月22日周五 上午1:50写道：

Hi,

Thanks so much for your help! I attached the matrix for you.

By the way, the input matrix should be TPM, log2 TPM or read counts? ST_mel1_rep1_log2tpm.txt https://github.com/tdw1221/NITUMID/files/3878261/ST_mel1_rep1_log2tpm.txt

— You are receiving this because you commented. Reply to this email directly, view it on GitHub https://github.com/tdw1221/NITUMID/issues/1?email_source=notifications&email_token=ADX7LO3OL4A2CW4CRERVTE3QU56JRA5CNFSM4JPNNVIKYY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOEE4XKBI#issuecomment-557413637, or unsubscribe https://github.com/notifications/unsubscribe-auth/ADX7LOYP7PQYPO7PZME7Z53QU56JRANCNFSM4JPNNVIA .

[tdw1221]

Here are my code

loading data

data_matrix <- read.table("~/project/Deconvolution/usr_feedback/ST_mel1_rep1_log2tpm.txt",sep="\t") data_matrix_num <- as.matrix(data_matrix)

transform from log to raw scale

data_matrix_num_raw <- 2^data_matrix_num

run NITUMID

output<-NITUMID(Y=data_matrix_num_raw )

output$result[[1]]$W

output$result[[1]]$H