User: russell.stewart.j

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Posts by russell.stewart.j

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Comment: C: DESeq2 Subsetting gives error in contrasts - can be applied only to factors with
... Thanks Michael, I rebuilt my dds and ran again without that factor like so and it worked: dds_Particle <- DESeqDataSetFromMatrix(countData = cts_df_ordered, colData = coldata_ordered_trim, design = ~ BMI + Diagnosis) dds_MP <- dds_Particle[, dds_Particle$Particle %in% c("MP")] dds_MP$Pa ...
written 10 months ago by russell.stewart.j0
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DESeq2 Subsetting gives error in contrasts - can be applied only to factors with 2 or more levels
... I'm running DESeq2 on a small RNA seq experiment. The coldata has 87 samples total and begins like this: Sample BMI Diagnosis Particle 1 Obese PCOS MP 10 Obese PCOS ...
deseq2 contrast multiple factor design written 10 months ago by russell.stewart.j0
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Comment: C: DESeq2 - couldn't find the function called DESeqDataSetFromMatrix
... I had this issue as well in RStudio when trying to knit RMarkdown code. I realized that the library can't be loaded independently of trying to knit the package. ...
written 17 months ago by russell.stewart.j0

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