User: Peter Alto

gravatar for Peter Alto
Peter Alto10
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10
Status:
New User
Location:
US/Chicago
Last seen:
11 months, 3 weeks ago
Joined:
1 year, 8 months ago
Email:
h***********@yahoo.com

Posts by Peter Alto

<prev • 4 results • page 1 of 1 • next >
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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 12 months ago by Peter Alto10 • updated 12 months ago by Michael Love16k
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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 20 months ago by Peter Alto10
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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 20 months ago by Peter Alto10
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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 20 months ago by Peter Alto10

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