User: new_user

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Posts by new_user

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Comment: C: Ballgown differential expression by exon problem
... Hi Alyssa. Thanks for the reply. I exported the mcov data using eexpr(bg_data,"mcov"). I have a data matrix with an additional column (rowVars of the proceeding columns containing the mcov data). I then filtered on row variance > 1 and performed the stattest as follows: numcols <- ncol(e_m ...
written 3 months ago by new_user0
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Comment: C: Ballgown differential expression by exon problem
... So after some digging it looks like the filter "rowVars(eexpr(bg_data_filt))>1" is not working. Even if I go back to the original unfiltered ballgown object (not filtering for low abundance transcripts first), and use: bg_data_filt_e <- ballgown::subset(bg_data, "rowVars(eexpr(bg_data, meas= ...
written 3 months ago by new_user0
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Ballgown differential expression by exon problem
... I am getting an error when running the following code using the Ballgown package: results_exons <-  stattest(bg_data_filt_e, feature='exon', covariate='Condition' , meas='mcov') The error is: Error in solve.default(t(mod) %*% mod) :   system is computationally singular: reciprocal condition nu ...
ballgown written 3 months ago by new_user0
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Comment: C: Ballgown Plotmeans problem
... Just checked and increasing replicate number to 3 allows plotting of means. I am assuming this is some hard coded limitation of ballgown. If anyone else is finding this and could comment just to confirm that would be appreciated. ...
written 3 months ago by new_user0
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Ballgown Plotmeans problem
... I am trying to use the ballgown Plotmeans function to display side-by-side plots of transcript level expression under 3 different experimental conditions (3 conditions with only 2 replicates per condition). I am using the following code: plotMeans("MSTRG.8",bg_data_filt,groupvar = "Condition", gro ...
ballgown written 3 months ago by new_user0

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