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giannimonaco / ABIS

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Running the algortihm locally #9

Closed drhmoosavi closed 4 years ago

drhmoosavi commented 4 years ago

Hi, I would like to run my microarrays gene expressions through the algorithm on my PC. I have savedthe repository but couldn't understand what to run in either the ui.R or the server.R files. I can see in server.R there are variables sigMicroarray , target , MedianTPM and Annotation that need the file location on the disk, which I changed to the correct path. What next? how to generate output file and where will it be saved ?

Thanks

giannimonaco commented 4 years ago

Hi,

to run the shiny app locally, you should open either the ui.R or the server.R file in R studio. RStudio will recognize the Shiny script and provide a Run App button (at the top of the editor). Either click this button to launch your app or use the keyboard shortcut: Command+Shift+Enter (Control+Shift+Enter on Windows).

Check also: https://shiny.rstudio.com/tutorial/written-tutorial/lesson1/

Best, Gianni

drhmoosavi commented 4 years ago

Thanks for the response. I did find out how to run the codes, however, I can't get over an warning R gives me after I upload my gene expression data using shiny interface. I am not sure where the results are correct. The warning is Warning in rlm.default(as.matrix(sigMicroarray[genes, ]), x) : 'rlm' failed to converge in 20 steps any idea? Thanks again.

giannimonaco commented 4 years ago

Hello,

can you try the last version of ABIS? It should not give you the warning in the last version.

Let me know, Gianni

On Tue, 17 Dec 2019 at 09:11, seymoo notifications@github.com wrote:

Thanks for the response. I did find out how to run the codes, however, I can't get over an warning R gives me after I upload my gene expression data using shiny interface. I am not sure where the results are correct. The warning is Warning in rlm.default(as.matrix(sigMicroarray[genes, ]), x) : 'rlm' failed to converge in 20 steps any idea? Thanks again.

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drhmoosavi commented 4 years ago

It worked! however, when I download the result, cell population names (in the row names) is missing in the txt file.

giannimonaco commented 4 years ago

Sorry, you are right. I fixed that too now!

On Tue, 17 Dec 2019 at 12:12, seymoo notifications@github.com wrote:

It worked! however, when I download the result, cell population names (in the row names) is missing in the txt file.

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giannimonaco commented 3 years ago

Hi, the results should still be good even if you get the warning. You could increase the value given to the maxit argument to avoid the warning.

On Sun, 6 Jun 2021 at 16:03, sam-israel @.***> wrote:

I have cloned the repo ( git clone https://github.com/giannimonaco/ABIS) and ran the Shiny app locally (with the default RNA seq signature matrix - on 400 samples).

I get a similar message to the user above

Warning in rlm.default(as.matrix(sigRNAseq[genes, ]), x, maxit = 100) : 'rlm' failed to converge in 100 steps

Is it important? Does it invalidate the deconvolution results? How can this be fixed?

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