Error in rowSums

[ofleitas]

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]

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]

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.

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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 <#20 (comment)>, 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]

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]

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?

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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 <#20 (comment)>, 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>. You are receiving this because you authored the thread.Message ID: ***@***.***>

[Russel88]

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]

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

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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 <#20 (comment)>, 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>. You are receiving this because you authored the thread.Message ID: ***@***.***>