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Russel88 / DAtest

Compare different differential abundance and expression methods
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Error in rowSums #20

Closed ofleitas closed 2 years ago

ofleitas commented 2 years ago

Hello

I am trying to analyse RNA-seq data with testDA function but i get this return :

606 empty features removed Running on 3 cores predictor is assumed to be a categorical variable with 6 levels: ct1, ct2, ct3, rst1, rst2, rst3 Spikeing... Error in rowSums(count_table[, predictor == 1]) : 'x' must be an array of at least two dimensions

Russel88 commented 2 years ago

Hi ofleitas,

I need some more information to figure out what's going on. How many samples and features are in your input? Are you using phyloseq as input or a data.frame?

ofleitas commented 2 years ago

Hello My input contains 6 samples, 3 from a control condition and 3 from a treatment condition and the features are 5799. I am using a data frame as input.

On Thu, Dec 16, 2021 at 2:38 AM Jakob Russel @.***> wrote:

Hi ofleitas,

I need some more information to figure out what's going on. How many samples and features are in your input? Are you using phyloseq as input or a data.frame?

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub https://github.com/Russel88/DAtest/issues/20#issuecomment-995555244, or unsubscribe https://github.com/notifications/unsubscribe-auth/AM624NDXNLZ24IE5NMTRIULURGQQHANCNFSM5KE3RFLQ . Triage notifications on the go with GitHub Mobile for iOS https://apps.apple.com/app/apple-store/id1477376905?ct=notification-email&mt=8&pt=524675 or Android https://play.google.com/store/apps/details?id=com.github.android&referrer=utm_campaign%3Dnotification-email%26utm_medium%3Demail%26utm_source%3Dgithub.

Russel88 commented 2 years ago

I looks like your predictor variable is wrong. The output says ct1, ct2, ct3, rst1, rst2, rst3. Your predictor should have the same value for all controls and same value for all treatments. Else it looks like there are six conditions with only 1 sample in each

ofleitas commented 2 years ago

Thank you very much for the reply. Is there a predictor file available that can be used as an example so that users can be guided in its preparation?

On Thu, Dec 23, 2021 at 6:29 AM Jakob Russel @.***> wrote:

I looks like your predictor variable is wrong. The output says ct1, ct2, ct3, rst1, rst2, rst3. Your predictor should have the same value for all controls and same value for all treatments. Else it looks like there are six conditions with only 1 sample in each

— Reply to this email directly, view it on GitHub https://github.com/Russel88/DAtest/issues/20#issuecomment-1000272024, or unsubscribe https://github.com/notifications/unsubscribe-auth/AM624NGLMHEPL5CUYPT3FFDUSMIZHANCNFSM5KE3RFLQ . Triage notifications on the go with GitHub Mobile for iOS https://apps.apple.com/app/apple-store/id1477376905?ct=notification-email&mt=8&pt=524675 or Android https://play.google.com/store/apps/details?id=com.github.android&referrer=utm_campaign%3Dnotification-email%26utm_medium%3Demail%26utm_source%3Dgithub.

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Russel88 commented 2 years ago

I don't have an example, unfortunately. But in your case it could be predictor = c("ct", "ct", "ct", "rst", "rst", "rst"), if that matches the order of the columns in the input data.frame.

ofleitas commented 2 years ago

Hello

Thank you very much for the suggestion, the analysis worked well.

On Thu, Dec 23, 2021 at 7:42 AM Jakob Russel @.***> wrote:

I don't have an example, unfortunately. But in your case it could be predictor = c("ct", "ct", "ct", "rst", "rst", "rst"), if that matches the order of the columns in the input data.frame.

— Reply to this email directly, view it on GitHub https://github.com/Russel88/DAtest/issues/20#issuecomment-1000313683, or unsubscribe https://github.com/notifications/unsubscribe-auth/AM624NGLFWTTZICMHK4FOZ3USMRLZANCNFSM5KE3RFLQ . Triage notifications on the go with GitHub Mobile for iOS https://apps.apple.com/app/apple-store/id1477376905?ct=notification-email&mt=8&pt=524675 or Android https://play.google.com/store/apps/details?id=com.github.android&referrer=utm_campaign%3Dnotification-email%26utm_medium%3Demail%26utm_source%3Dgithub.

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