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mani2012 / BatchQC

Provides Quality Control of sequencing samples by deducing if there is batch effect and adjusts for it.
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Download corrected data #19

Open cadyyuheng opened 3 years ago

cadyyuheng commented 3 years ago

Hi,

Thanks for sharing this wonderful package. I was wondering if I could download the combat corrected expression matrix from the shiny page.

Thanks!

mani2012 commented 3 years ago

Hi,

No, there is no option to directly download the combat corrected data from the shiny page. You will have to manually call the ComBat function for that.

Best, Mani

From: cadyyuheng notifications@github.com Sent: Thursday, October 15, 2020 5:28 PM To: mani2012/BatchQC BatchQC@noreply.github.com Cc: Subscribed subscribed@noreply.github.com Subject: [mani2012/BatchQC] Download corrected data (#19)

Hi,

Thanks for sharing this wonderful package. I was wondering if I could download the combat corrected expression matrix from the shiny page.

Thanks!

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cadyyuheng commented 3 years ago

Mani,

Thanks for your reply. I tried to run ComBat myself, but I got pretty different PCA results as the ones I got from doing ComBat on BatchQC. I'm trying to figure out the source of such variations. Are there any possible causes on top of your mind?

Thanks

mani2012 commented 3 years ago

Hi,

You may have to check the options used.

Best, Mani

From: cadyyuheng notifications@github.com Sent: Thursday, October 15, 2020 11:55 PM To: mani2012/BatchQC BatchQC@noreply.github.com Cc: Solaiappan Manimaran manimaran_1975@hotmail.com; Comment comment@noreply.github.com Subject: Re: [mani2012/BatchQC] Download corrected data (#19)

Mani,

Thanks for your reply. I tried to run ComBat myself, but I got pretty different PCA results as the ones I got from doing ComBat on BatchQC. I'm trying to figure out the source of such variations. Are there any possible causes on top of your mind?

Thanks

— You are receiving this because you commented. Reply to this email directly, view it on GitHubhttps://github.com/mani2012/BatchQC/issues/19#issuecomment-709715682, or unsubscribehttps://github.com/notifications/unsubscribe-auth/ACMB4PH36Z42N5WOVJ544WDSK67YHANCNFSM4SSQXL7A.

gun-hub commented 3 years ago

Hi,

I have the same query as asked by cadyyuheng. I also need ComBat corrected data for further processing. I tried your suggestion by running Combat independently with the parameters used in BatchQC, but the PCA plot of the output file was entirely different. Can you please suggest what else could be different in the output files corrected file generated by BatchQC and independent ComBat script run?

Thanks

mani2012 commented 3 years ago

You may have to check the options used when running ComBat:

    combat_data <- ComBat(dat=shinyInput$lcounts, batch=shinyInput$batch,
        mod = mod, par.prior = par.prior, mean.only = mean.only)

Also check whether you are using additional log2cpm_transform option.

From: gun-hub @.> Sent: Thursday, June 10, 2021 7:48 PM To: mani2012/BatchQC @.> Cc: Solaiappan Manimaran @.>; Comment @.> Subject: Re: [mani2012/BatchQC] Download corrected data (#19)

Hi,

I have the same query as asked by cadyyuheng. I also need ComBat corrected data for further processing. I tried your suggestion by running Combat independently with the parameters used in BatchQC, but the PCA plot of the output file was entirely different. Can you please suggest what else could be different in the output files corrected file generated by BatchQC and independent ComBat script run?

Thanks

— You are receiving this because you commented. Reply to this email directly, view it on GitHubhttps://github.com/mani2012/BatchQC/issues/19#issuecomment-859158842, or unsubscribehttps://github.com/notifications/unsubscribe-auth/ACMB4PGCKKDZIBTIEJE4UE3TSFFJ5ANCNFSM4SSQXL7A.