Comments (2)
JEFworks
commented on June 17, 2024
It looks like for your grouping vector, you are setting some cells to NA then converting that vector into a factor so ‘NA’ is being treated as a factor grouping. You will need to convert to a factor first, then set cells to NA such that levels(grouping_factor) only has 2 levels.
ex.
> groups <- factor(gsub("(MEF|ESC).*", "\\1", rownames(o.ifm)), levels = c("ESC", "MEF"))
> names(groups) <- row.names(o.ifm)
>
> groups
ESC_10 ESC_11 ESC_12 ESC_13 ESC_14 ESC_15 ESC_16 ESC_17 ESC_18 ESC_19 ESC_1 ESC_20
ESC ESC ESC ESC ESC ESC ESC ESC ESC ESC ESC ESC
ESC_21 ESC_22 ESC_23 ESC_24 ESC_25 ESC_26 ESC_27 ESC_28 MEF_49 MEF_50 MEF_51 MEF_52
ESC ESC ESC ESC ESC ESC ESC ESC MEF MEF MEF MEF
MEF_53 MEF_54 MEF_55 MEF_56 MEF_57 MEF_58 MEF_59 MEF_60 MEF_61 MEF_62 MEF_63 MEF_64
MEF MEF MEF MEF MEF MEF MEF MEF MEF MEF MEF MEF
MEF_65 MEF_66 MEF_67 MEF_68
MEF MEF MEF MEF
Levels: ESC MEF
> groups[1] <- NA
> groups
ESC_10 ESC_11 ESC_12 ESC_13 ESC_14 ESC_15 ESC_16 ESC_17 ESC_18 ESC_19 ESC_1 ESC_20
<NA> ESC ESC ESC ESC ESC ESC ESC ESC ESC ESC ESC
ESC_21 ESC_22 ESC_23 ESC_24 ESC_25 ESC_26 ESC_27 ESC_28 MEF_49 MEF_50 MEF_51 MEF_52
ESC ESC ESC ESC ESC ESC ESC ESC MEF MEF MEF MEF
MEF_53 MEF_54 MEF_55 MEF_56 MEF_57 MEF_58 MEF_59 MEF_60 MEF_61 MEF_62 MEF_63 MEF_64
MEF MEF MEF MEF MEF MEF MEF MEF MEF MEF MEF MEF
MEF_65 MEF_66 MEF_67 MEF_68
MEF MEF MEF MEF
Levels: ESC MEF
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ulah
commented on June 17, 2024
yes, that was the problem, thanks!
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