Input and Output

[Winnie09]

Dear author,

Thanks for developing the software! I have a few questions but did not find clear answer from your paper:

1. is the input a count matrix?
2. is the output a count matrix? Has it been normalized by library size, or log2-transformed?

Thanks!

[linqiaozhi]

Hi @Winnie09, we use the normalize_data() function to convert the count matrix into a library size and log transformed matrix. We have not explored the effects of not normalizing or not doing the log transform, however.

The output can be considered to have the same "transformation" done to it as the input data. The alra() function itself does not actually do any normalization, but if the input data was normalized, then the imputed data will have roughly the same distribution.

[Winnie09]

This is very helpful. Thanks a lot! On Mar 20, 2019, at 10:01 AM, George Linderman <notifications@github.com<mailto:notifications@github.com>> wrote: Hi @Winnie09<https://github.com/Winnie09>, we use the normalize_data() function to convert the count matrix into a library size and log transformed matrix. We have not explored the effects of not normalizing or not doing the log transform, however. The output can be considered to have the same "transformation" done to it as the input data. The alra() function itself does not actually do any normalization, but if the input data was normalized, then the imputed data will have roughly the same distribution. — You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub<#3 (comment)>, or mute the thread<https://github.com/notifications/unsubscribe-auth/AV0rVZ3XrY88kYNN4jKZXNHRpD4rexmFks5vYj8ugaJpZM4b6nAB>.

[chatterjee89]

Hi @linqiaozhi I have a quick question related to this one:
Would you recommend applying ALRA to impute scaled data or raw data in the count matrix?
Thank you so much for the question and the software.

FYI, I'm applying this on scRNA Seq data being analyzed on Seurat.

Regards,
Deep