Error in SubMap

[xf627...@gmail.com]

Hi there,

 

I follow the instruction and made a label stating with 1 in 3^rd line but I always get error :

 

Error in if (min(as.numeric(cls)) == 0) { :

                missing value where TRUE/FALSE needed

Execution halted

 

Attached is one of my cls file, all parameters are set default.

could anyone give me some help.

 

Thank you so much!

Btw, I am not sure if this is a job ID : 1689448. SubMap 

[xf627...@gmail.com]

Hello, anyone can help???

I have tried tons of times....all ERROR

在 2018年6月8日星期五 UTC-5下午3:00:32，xf627...@gmail.com写道：

[Barbara Hill]

Hello,

Apologies for the delay in responding. 

Unfortunately, your job has been purged, as it has been over a week. So, I can't look at your input data.

Might it have had features that are zero or "flat" across all columns?

Best

-Barbara

[xf627...@gmail.com]

Hi Barbara,

I will try again tomorrow and I think I will still get en error. Hope this time you can check the input data.

在 2018年6月18日星期一 UTC-5下午4:26:46，Barbara Hill写道：

[xf627...@gmail.com]

Good Morning,

The new ID is 1696733 and yes it is still an error.

在 2018年6月18日星期一 UTC-5下午4:26:46，Barbara Hill写道：

Hello,

[Barbara Hill]

Hello

It does look like you have some rows which may be interpreted as flat by the algorithm:

For example in your dataseta.file, rows 14, 196 and 242 contain a majority of 0 values, and row 757 is all 0s.

Best

-Barbara

[xf627...@gmail.com]

Thank you.

However, I still get error when I filtered low expressed genes.

My work ID is 1698087 this time.

The flat value maybe one reason, but, as I mentioned, the error information is :

Error in if (min(as.numeric(cls)) == 0) { : 
	missing value where TRUE/FALSE needed
Execution halted

Thus, I think it is concerning about the cls file.

Could you check it for me?

Thank you so much.

在 2018年6月28日星期四 UTC-5下午12:31:25，Barbara Hill写道：

[Barbara Hill]

Hello, 

I'm just returning from vacation and, unfortunately, your job has been purged. Please run it again and provide a new job id for me to review.

Best

-Barbara

[6279...@qq.com]

Ok.
The new job ID is 1704645 and the error is still

Error in if (min(as.numeric(cls)) == 0) { :
    missing value where TRUE/FALSE needed
Execution halted

Please advise.
Best.

在 2018年7月17日星期二 UTC+8上午1:24:21，Barbara Hill写道：

[6279...@qq.com]

Ok I know the last job is going to be purged and actually, I do not know how long I should wait for getting the solution.
Thus this is the new job ID:
1706368

Many thanks.

在 2018年7月17日星期二 UTC+8上午1:24:21，Barbara Hill写道：

Hello, 

[Barbara Hill]

Hello, 

Thank you for the updated job id - I'm running through some tests now to see if I can help.

Best

-Barbara

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Barbara Hill
Senior Test Engineer

GenePattern Product Owner

Informatics Development
Broad Institute of MIT and Harvard

415 Main St, Cambridge, MA 02142, USA

email: bh...@broadinstitute.org
phone: 617-714-7508
http://genepattern.org

[Barbara Hill]

Hello again, 

I fixed your files as follows:

Removed extra spaces from the end of your cls files and updated the first line to only have 1 space between each number.

For the GCT files - they were incorrectly formatted.

GCT files should have a description column as the second column - this is optionally populated, but it impacts the dimensions of the matrix. This increased your number of samples in each file by 1 which brought the number of samples in your gct files in line with the number of samples indicated in your cls files.

I have shared my job with you, so that you can download the files, or simply reload the job and run it to get the same job run by your user.

https://genepattern.broadinstitute.org/gp/pages/index.jsf?jobid=1706975&openNewWindow=false

Best

-Barbara

[6279...@qq.com]

Thank you soooooooooooooo much!

在 2018年7月25日星期三 UTC+8上午5:25:01，Barbara Hill写道：