User: nickp60

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nickp600
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Posts by nickp60

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Comment: C: Extracting custom post-normalization counts from DESeq2
... Fair enough-  thanks again for all the help! ...
written 3.4 years ago by nickp600
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Comment: C: Extracting custom post-normalization counts from DESeq2
... Hi Michael;  thank you, that is helpful.  could you explain a bit more about the removeBatchEffect() function call?  When I run the function with batch=pData$W_1, the columns of the resulting dataframe are identical.  Do I need to adjust the default design argument?  And if so, how? ...
written 3.4 years ago by nickp600
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Answer: A: Extracting custom post-normalization counts from DESeq2
... At risk of painting a giant target on my head for posting a pokey for-loop solution, I have a workaround that fits my needs for now.  This little snippet utilizes a modified version of the plotCounts function.   make a duplicate function of plotCounts called plotCounts2 replace : if (is.null( ...
written 3.4 years ago by nickp600
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Comment: C: Extracting custom post-normalization counts from DESeq2
... Hi @Michael,  Thanks for your reply;  I look forward to the release of this feature.   (previous content removed due to calculation error) ...
written 3.4 years ago by nickp600
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Extracting custom post-normalization counts from DESeq2
... Hi, I am experimenting with different normalization techniques to account for batch effects on an RNAseq dataset.  I am using DESeq2 for DE analysis, and RUVseq for normalization.  For plotting purposes, I want to be able to extract the post-normalization counts (pseudocounts?) from the DESeqDataSe ...
rnaseq normalization deseq2 ruvseq R written 3.4 years ago by nickp600
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Answer: A: Recent problem with biomaRt query
... A little more digging reveals that the database I have been using had been part of a proteome culling effort to reduce redundency.  See the link below for more info.  http://www.uniprot.org/uniprot/A8YZ21 ...
written 3.5 years ago by nickp600
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Recent problem with biomaRt query
... Has anyone run into issues recently with sumitting biomaRt queries?  I am submitting a list of bacterial gene accessions to uniprot dataset and returning GO ID's.  Last month, with the same list of ~384 genes, I was returning a list of about 500 GO Terms.  Now, I get around 250 GO Terms. Was there a ...
biomart R rstudio written 3.5 years ago by nickp600

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Popular Question 3.4 years ago, created a question with more than 1,000 views. For Extracting custom post-normalization counts from DESeq2

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