User: agdif

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agdif0
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Posts by agdif

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DESeq2: Extract mean normalized log2 counts by level
... Hi, I currently am using a dataset with 5 timepoints and 4 replicates per timepoint. While the results file exports the L2FC, I am also interested in extracting the numerator log2 values for each time point. I have already extracted the log2 normalized counts for each individual sample with the cod ...
log2 normalized counts written 5 weeks ago by agdif0
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DESeq2: likelihood ratio test interpretation, multifactor
... Hi Michael, I would like to make sure that I am interpretating the p-values correctly when using the likelihood ratio test with a multifactor design. We are interested in identifying significant genes that are differentially expressed between 3 disease states while controlling for sex. I understan ...
deseq2 lrt likelihood ratio test written 9 weeks ago by agdif0 • updated 9 weeks ago by Michael Love19k
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biomaRt getBM() function does not recognize gene ID character vector values generated from csv file for annotation
... I have a multi-column csv file. In the first column are ensembl IDs that I would like to annotate using biomaRt in RStudio. After reading the csv file into R as a dataframe I have converted the first column with the IDs to a character vector, since the getBM() parameter, values, requires a list of ...
annotation biomart ensembl csv files getbm() written 3 months ago by agdif0 • updated 3 months ago by Mike Smith3.0k
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Comment: C: Better to use rlog or vst transformation for data quality assessment of differen
... Thanks Michael!  ...
written 4 months ago by agdif0
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Better to use rlog or vst transformation for data quality assessment of differental expression data based on size factors?
... Hello, I finished running DESeq2 on my dataset that includes 6 timepoints and 3 biological replicates per timepoint. I would like to run a PCA analysis for quality assessment but am unsure which count transformation method I should use, vst or rlog.  The calculated the size factors for my dataset ...
deseq2 rlog transformation vst quality assesment written 4 months ago by agdif0 • updated 4 months ago by Michael Love19k

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