User: JunLVI

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JunLVI40
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Japan
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4 months ago
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Posts by JunLVI

<prev • 47 results • page 1 of 5 • next >
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Comment: C: Global reduction of epigenetic factors (regularized log transformation DESeq2)
... @Michal Love, thanks very much for your suggestions. I will try a set of house keeping genes ( here those gene associated epigenomic loci).  it seems to me that some prior evidences /knowledges / assumptions are needed to decide which is the best way to normalize the datasets.  Devon recommended t ...
written 18 months ago by JunLVI40
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Answer: A: Global reduction of epigenetic factors (regularized log transformation DESeq2)
...     @Michael Love, I have posted the question related to DiffBind, has yet to receive any feedback. but I have found some related posts,  in replying " DiffBind dba.report() output: Is "concentration" normalized?" Rory explained, "the counts are normalized. Concentrations are reported as log2 va ...
written 18 months ago by JunLVI40
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DiffBind :Retrieve count value from Diffbind by dab.report
...   I have questions about "dba.report", I applied "DiffBind" to analyze my dataset like:   H3K27ac_CellA_CellD <- dba(sampleSheet="sampleconfiguration.csv",) H3K27ac_CellA_CellD_Count <- dba.count(H3K27ac_CellA_CellD, score= DBA_SCORE_TMM_READS_EFFECTIVE, mapQCth=0, bRemoveDuplicates=FALSE ...
diffbind written 18 months ago by JunLVI40 • updated 18 months ago by Rory Stark2.6k
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Comment: C: Global reduction of epigenetic factors (regularized log transformation DESeq2)
... @Michael Love,  Thanks to your suggestion, I went back to check my original code:  Here is code in R session:   H3K27ac_CellA_CellD <- dba(sampleSheet="sampleconfiguration.csv",) H3K27ac_CellA_CellD_Count <- dba.count(H3K27ac_CellA_CellD, score= DBA_SCORE_TMM_READS_EFFECTIVE, mapQCth=0, bR ...
written 18 months ago by JunLVI40
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Comment: C: Global reduction of epigenetic factors (regularized log transformation DESeq2)
... @Michael Love, Hi, Michael, thank you very much for your feedback. Yes, the rlog-ed values are plotted, sorry that I did not make that clear.  I checked the "estimateSizeFactors" documentations,  I guess the "control gene" argument is what you mean by "you can provide whatever size factors you like ...
written 18 months ago by JunLVI40
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Global reduction of epigenetic factors (regularized log transformation DESeq2) ~ Diffbind
... Hi, I was trying to investigate the changes of H3K27ac upon conditional KO of gene X. After mapping and counting the data using "featurecount" from "Rsubread" packages, I used the DEseq2 to perform differential analysis.  Below is the scatter plot (WT vs CKO), I could obtain genomic region with th ...
diffbind deseq2 written 18 months ago by JunLVI40 • updated 18 months ago by Michael Love20k
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Comment: C: How to determine means for rlog value of biological duplicates calculated by DES
... @Michael Love, answer straightforward enough, thanks! ...
written 20 months ago by JunLVI40
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How to determine means for rlog value of biological duplicates calculated by DESeq2
... Hi. I have used DESeq2 to performed differential analysis.  And now I would like to plot the data using transformed values "rld", but not sure how to determine the means for the biological duplicates. The simplest way I could think of is use the arithmetic means. For normal log transformation, that ...
deseq2 written 20 months ago by JunLVI40 • updated 20 months ago by Michael Love20k
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Comment: C: Issue when import genomic features from the file :Error in parseURI("") : cannot
... @Mike Smith. Hi Mike, thank you very much.Thanks to you and Martin,  I guess that I am set now.  Despite the fact that I had the error print out during installation, when I checked today (it is always good to check again the next day...)    > library("XML") > XML::parseURI("") $scheme [1] ...
written 21 months ago by JunLVI40
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Comment: C: Issue when import genomic features from the file :Error in parseURI("") : cannot
... Hi Mike. I guess  that I managed to install the libxml2, but something remains missing.If you have any idea, eager to know. TKS!   ./configure --prefix=$HOME/Programme --disable-static --with-history --with-zlib=/somewhere/Jun/Programme/zlib-1.2.11 && make make install # http://www.linux ...
written 21 months ago by JunLVI40

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