User: russell.stewart.j

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Posts by russell.stewart.j

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Should I subsample an over-clustered sample for DESeq2?
... We are performing a small RNA seq experiment and had one sample over cluster by about 5-fold compared to the rest of the libraries. With the intention of using DESeq2 after processing the data, would you suggest subsampling to match the rest of the sample depths, or will DESeq2 handle the scaling fi ...
deseq2 written 4 months ago by russell.stewart.j0 • updated 4 months ago by Michael Love25k
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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 17 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 17 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 2.0 years ago by russell.stewart.j0

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