Datasets

[cwyoo]

Dr. Yoo,

Please find the two datasets below. I added the JPEG file for the first run for the Cell Cycle. I'm already started running the second Banjo analysis for Cell Cycle.

Variable names should be shown. I only see variable's number ids.

[meninonas]

Dr. Yoo,

Please find the Cell Cycle dataset below with the first two Banjo analyses.

[cwyoo]

This is TGCA 2012 Breast Cancer dataset all merged.

[meninonas]

Dr. Yoo,

I have coded the datasets according to Mutation, Amplification, and Expression. I was not able to merge them in one large dataset due to LibreOffice Calc not being able to open the original dataset in its entirety. LibreOffice Calc gives me the following error:

Code: Select all

The data could not be loaded completely because the maximum number of columns per sheet was exceeded.

I would suggest opening the datasets in Microsoft Office if you have it available to you.

I am currently working on labeling the genes according to _MUT, _AMP, and _EXP. Those should be ready tomorrow.

[meninonas]

Dr. Yoo,

I ran the dataset in banjo and it gave me the following error:

Code: Select all

[ERROR: Banjo 2.2.0, 2/11/15 5:06:39 PM]
Execution has stopped because Banjo has run out of available memory.
'java.lang.OutOfMemoryError: Java heap space'

I ran banjo in 131.94.9.17 and it gave me the same error. When I tried accessing the other servers but I wasn't able to.

[cwyoo]

Dr. Yoo,

I ran the dataset in banjo and it gave me the following error:

Code: Select all

[ERROR: Banjo 2.2.0, 2/11/15 5:06:39 PM]
Execution has stopped because Banjo has run out of available memory.
'java.lang.OutOfMemoryError: Java heap space'

I ran banjo in 131.94.9.17 and it gave me the same error. When I tried accessing the other servers but I wasn't able to.

I have told you to match the id before merging the clinical data with expression data. You have used the clinical data that is sorted by "Subtype".

[meninonas]

Dr. Yoo,

Please find the Merged dataset below. Regardless, the size of the file remains the same and the number of columns went to 2841, which is an increase of about 700 columns. Consequently, the issue remains the same, both datasets are too large for the memory capacity.

[cwyoo]

Dr. Yoo,

Please find the Merged dataset below. Regardless, the size of the file remains the same and the number of columns went to 2841, which is an increase of about 700 columns. Consequently, the issue remains the same, both datasets are too large for the memory capacity.

What is the source of the error? Please post a file without any errors. What is the dimension of the original data that I post? After removing clinical variables and gene variables (state the reason why you deleted the variables), what is the dimension?

[meninonas]

What is the source of the error? Please post a file without any errors. What is the dimension of the original data that I post? After removing clinical variables and gene variables (state the reason why you deleted the variables), what is the dimension?

Dr. Yoo,

I tried calling you through Skype but you didn't answer.

I'm a little confused about the questions you asked in the post above. The error that banjo gave me is that the computer doesn't have enough memory to deal with the size of the dataset. I have re-added the error below:

Code: Select all

[ERROR: Banjo 2.2.0, 2/13/15 1:29:11 PM]
Execution has stopped because Banjo has run out of available memory.
'java.lang.OutOfMemoryError: Java heap space'

Consequently, I'm lead to believe that this computer does not have the capacity to deal with datasets that contain 2000+ columns.

When you say to post a file without errors, what are you referring to? To my knowledge, none of the datasets have errors in them.

The original data that you posted (TGCA_2012_all_merged.csv) has dimensions of 463x2162.

The reason why the Merged, Amplified, and Mutated Datasets do not contain the clinical variables is because we had a greed to first code the genes and then we would choose which clinical variables were going to be coded. I'm assuming the only clinical variables you're interested in having are the highlighted ones you sent me through email. The dataset you sent me through email is attached below. None of the genes were deleted.

[cwyoo]

What is the source of the error? Please post a file without any errors. What is the dimension of the original data that I post? After removing clinical variables and gene variables (state the reason why you deleted the variables), what is the dimension?

Dr. Yoo,

I tried calling you through Skype but you didn't answer.

I'm a little confused about the questions you asked in the post above. The error that banjo gave me is that the computer doesn't have enough memory to deal with the size of the dataset. I have re-added the error below:

Code: Select all

[ERROR: Banjo 2.2.0, 2/13/15 1:29:11 PM]
Execution has stopped because Banjo has run out of available memory.
'java.lang.OutOfMemoryError: Java heap space'

Consequently, I'm lead to believe that this computer does not have the capacity to deal with datasets that contain 2000+ columns.

When you say to post a file without errors, what are you referring to? To my knowledge, none of the datasets have errors in them.

The original data that you posted (TGCA_2012_all_merged.csv) has dimensions of 463x2162.

The reason why the Merged, Amplified, and Mutated Datasets do not contain the clinical variables is because we had a greed to first code the genes and then we would choose which clinical variables were going to be coded. I'm assuming the only clinical variables you're interested in having are the highlighted ones you sent me through email. The dataset you sent me through email is attached below. None of the genes were deleted.

If we started with 463×2162 and added several clinical variables, how can you end up with 2800+ columns?

Use expression data and include only limited number of genes that are highly correlated with NRF1. Start from 2,000 genes and check whether banjo runs in path-four, if not, each time remove 500 genes that are less correlated with NRF1 and check whether banjo runs.