User: Peter Alto

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Peter Alto0
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Posts by Peter Alto

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How to remove genes with 0 counts in tximport?
... Looking at the DESeqDataSetFromTximport() and tximport() functions, I can't find how to set a minimum number of reads per gene, which is necessary for correction of batch effects and recommended for differential expression. How can I filter genes using tximport? Thank you. ...
deseq deseq2 tximport tximportdata written 9 months ago by Peter Alto0 • updated 9 months ago by Michael Love15k
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Comment: C: PCA of svaseq "cleaned" counts and DESeq2 SV subtracted counts are different?
... Thanks for catching that, I fixed it. ...
written 17 months ago by Peter Alto0
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Answer: A: PCA of svaseq "cleaned" counts and DESeq2 SV subtracted counts are different?
... Thank you very much for your replies. I apologize for missing the information about rlog in the vignette. I read the post about removeBatchEffect and I'll try to use the covariates option to remove SV's estimated by svaseq. ...
written 17 months ago by Peter Alto0
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PCA of svaseq "cleaned" counts and DESeq2 SV subtracted counts are different?
... I am using svaseq and DESeq2 together to remove surrogate variables from an RNA-seq dataset and call DEG. I ran the raw counts through DESeq2 and rlog transformed the data for processing by svaseq. dds <- DESeqDataSetFromMatrix(countData = counts, colData = colData, design = ~ condition) dds &l ...
sva deseq2 pca svaseq written 17 months ago by Peter Alto0

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