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rhondabacher / SCnorm

Normalization for single cell RNA-seq data
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Example code ran with error #16

Closed SharonWang closed 7 years ago

SharonWang commented 7 years ago

Hi,

With the current version of SCnorm 0.99.3, I tried the following code in the user manu:

data(ExampleData) Conditions = rep(c(1), each= 90) DataNorm <- SCnorm(ExampleData, Conditions, OutputName = "MyNormalizedData", SavePDF=TRUE, FilterCellNum = 10, NCores=3)

However, it came up with the following error: Gene filter is applied within each condition. 0 genes were not included in the normalization due to having less than 10 non-zero values. A list of these genes can be accessed in output, see vignette for example. Finding K for Condition 1 Trying K = 1 Error in clara(as.matrix(Slopes), K) : x is not a numeric dataframe or matrix.

I tried to debug the code, and it seems that the SlopesList from the GetSlopes function put most of the genes into NA values.

It would be very appreciated and helpful if you could please check what happened.

Best regards,

Xiaonan Wang

rhondabacher commented 7 years ago

Hi Xiaonan,

Thank you for using SCnorm. I removed my previous versions and reinstalled 0.99.3, but was not able to reproduce the error you received. Have you tried reinstalling via:

library(devtools) devtools::install_github("rhondabacher/SCnorm")

Please let me know if that does not resolve the issue.

Best, Rhonda

On Wed, Jul 12, 2017 at 10:25 AM, SharonWang notifications@github.com wrote:

Hi,

With the current version of SCnorm 0.99.3, I tried the following code in the user manu:

data(ExampleData) Conditions = rep(c(1), each= 90) DataNorm <- SCnorm(ExampleData, Conditions, OutputName = "MyNormalizedData", SavePDF=TRUE, FilterCellNum = 10, NCores=3)

However, it came up with the following error: Gene filter is applied within each condition. 0 genes were not included in the normalization due to having less than 10 non-zero values. A list of these genes can be accessed in output, see vignette for example. Finding K for Condition 1 Trying K = 1 Error in clara(as.matrix(Slopes), K) : x is not a numeric dataframe or matrix.

I tried to debug the code, and it seems that the SlopesList from the GetSlopes function put most of the genes into NA values.

It would be very appreciated and helpful if you could please check what happened.

Best regards,

Xiaonan Wang

— You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub https://github.com/rhondabacher/SCnorm/issues/16, or mute the thread https://github.com/notifications/unsubscribe-auth/AGTh7Fp0rErmPRqw_I37ixPtQzXjDxGiks5sNOVWgaJpZM4OVzG8 .

-- Rhonda Bacher, PhD Department of Biostatistics Biotechnology Center (2130) 425 Henry Mall University of Wisconsin-Madison Email: rbacher@wisc.edu Website: https://rhondabacher.github.io

SharonWang commented 7 years ago

Dear Rhonda,

Thanks a lot for the quick reply.

I figured out the issue which was because the SparseM package was not updated to the latest version.

Now it runs fine.

Best regards,

Xiaonan Wang