User: luca.rugiu

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luca.rugiu0
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Posts by luca.rugiu

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Comment: C: Problem making DESeq dataset; Error all variables in design formula must be colu
... ok, it works! thanks a lot for your help and patience! have a good day -Luca ...
written 6 months ago by luca.rugiu0
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Comment: C: Problem making DESeq dataset; Error all variables in design formula must be colu
... I see.  I found from the link I previously provided that nested designs need some extra coding.  In that guide, this is suggested: model.matrix(~ grp + grp:ind.n + grp:cnd, coldata), so that nested effects among groups could be taken into account. From this point, how do I get to DE analysis if ...
written 6 months ago by luca.rugiu0
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Comment: C: Problem making DESeq dataset; Error all variables in design formula must be colu
... Also, I had to type "colnames(cts) <- NULL" to avoid an error as found out in an other post, so the colnames of my countData are now null. Not sure this is relevant...         [,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,10] [,11] [,12] [,13] [,14] TRINITY_DN293388_c0_g1    0    7    0    1    ...
written 6 months ago by luca.rugiu0
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Comment: C: Problem making DESeq dataset; Error all variables in design formula must be colu
... Thanks a lot for the quick reply. colnames(mat2) (Intercept)"         "grpSeili"            "grpRauma:ind.nb"     "grpSeili:ind.nb"   "grpRauma:ind.nc"     "grpSeili:ind.nc"     "grpRauma:ind.nd"     "grpRauma:cndpresent"  "grpSeili:cndpresent"   when trying to replace cond with one of the colna ...
written 6 months ago by luca.rugiu0
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Comment: C: Problem making DESeq dataset; Error all variables in design formula must be colu
... Hello,  I got the same error "Error in DESeqDataSet(se, design = design, ignoreRank) :    all variables in design formula must be columns in colData" my code is: fulldds <- DESeqDataSetFromMatrix(countData = cts, colData = mat2, design = ~ cnd) I am trying to estimate group effect using a nes ...
written 6 months ago by luca.rugiu0

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