User: arielle

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arielle0
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Posts by arielle

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Comment: C: DESeq2: Contrasts in multifactor design with interaction terms
... I added that line to clarify it. I will try doing what you suggested. I am a beginner with using model matrices and contrasts, so this is why I wanted to make sure that I am doing it properly. ...
written 4 weeks ago by arielle0
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Comment: C: DESeq2: Contrasts in multifactor design with interaction terms
... Edited my reply for typos ...
written 4 weeks ago by arielle0
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Comment: C: DESeq2: Contrasts in multifactor design with interaction terms
... (deleted, the same message posted twice) ...
written 4 weeks ago by arielle0
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Comment: C: DESeq2: Contrasts in multifactor design with interaction terms
... The point of starting with all interactions is not to guess the contrasts. I am developing a function that uses DESeq as part of it, but this function needs to be flexible and return a dds object from which the user can extract differential expression using the appropriate contrasts, and an example ...
written 4 weeks ago by arielle0
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DESeq2: Contrasts in multifactor design with interaction terms
... Hi, I have a design with three variables: tissue, time and phenotype, where the tissue has three levels (X, Y and Z, where X is the reference level), time as three levels (12h, 24h and 48h, where 12h is the reference level), and phenotype has three levels (ctrl, A and B, where ctrl is the reference ...
deseq2 R written 4 weeks ago by arielle0
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DESeq2: error, the model matrix is not full rank, linear combinations
... Hi, I am using DESeq2 with this model matrix (dput of the model matrix and DESeq2 command are pasted below). However, DESeq2 complains that some of the columns in the model matrix are linear combinations of each other (also see the error below). I am aware that this is an usual model matrix, but I d ...
deseq2 written 4 months ago by arielle0 • updated 4 months ago by Peter Langfelder2.1k
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Answer: A: SRAdb: Error downloading sqlite files
... It seems that the getSRAdbFile() function does not worked for me. This solved the problem: system("wget https://s3.amazonaws.com/starbuck1/sradb/SRAmetadb.sqlite.gz") system("gunzip SRAmetadb.sqlite.gz") sqlfile <- 'SRAmetadb.sqlite' ...
written 21 months ago by arielle0
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SRAdb: Error downloading sqlite files
...   I have successfully installed the SRAdb package. I am now trying to download and uncompress the files, sqlfile <- 'SRAmetadb.sqlite' if(!file.exists('SRAmetadb.sqlite')) sqlfile <<- getSRAdbFile() But I get the following error: downloaded 0 bytes Error in download.file(url_sra, d ...
sradb written 22 months ago by arielle0
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DESeq: How are condition A and B assigned
... I am using DESeq to perform differential expression analysis. I have read and followed the instructions in the user manuals. I am calling differential expression, using this type of command:  res = nbinomTest( cds, "untreated", "treated" ). I am assuming that untreated will be assigned as condition ...
deseq R written 2.6 years ago by arielle0

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Scholar 2.3 years ago, created an answer that has been accepted. For A: SRAdb: Error downloading sqlite files

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