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bhklab / genefu

R package providing various functions relevant for gene expression analysis with emphasis on breast cancer.
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About claudinLow function to analyze three groups of patients #23

Closed HengqiLiu closed 2 years ago

HengqiLiu commented 2 years ago

Hi "genefu" package team:

I have three groups of patients and plan to perform claudinLow analysis on them, but I find that such an error will be reported: Error in dimnames(x) <- dn : length of 'dimnames' [2] not equal to array extent.

When I use only two groups of patients, it works perfectly.

I found that the error is caused by these two lines of code of the claudinLow function

colnames(distances) <- c("euclidian distance to Claudin-low", "euclidian distance to Others")

What I want to know is if there is a way to perform claudinLow analysis on the three groups of patients.

Thank you !!

ChristopherEeles commented 2 years ago

Hi @HengqiLiu,

To help resolve your issue I need three pieces of information.

Firstly, please run the sessionInfo() function in your R console and provide the output here. This will give me the necessary background information about your R environment, such as which version of packages you are using.

Secondly, I need the exact code you are trying to execute to see which function options you are using.

Finally, I need a small subset of your input data to use for debugging. You can use the dput function return the code needed to make an R object. Please provide the input matrix you are using, as well as any additional data that you may be passing into the function. You can retrieve this information like this:

dput(head(x))

Where x is your input matrix to the claudinLow function. Then copy and paste the value and post it here.

Once I have this information I can try running your code and see what is going wrong.

Best, Christopher Eeles Software Developer BHK Lab | PM-Research | UHN

HengqiLiu commented 2 years ago

Hi Christopher Eeles:

Thank you for your prompt reply, and I apologize to you because my own data input mistake caused the error. I used my own patient group information as a train dataset insted of the claudinLowData dataset. After I corrected my mistake, the claudinLow function can run perfectly and output the result.

Thank you and your team for developing genefu tools.

Best, Henqi Liu