User: ZheFrench

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ZheFrench10
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2 months ago
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1 year, 1 month ago
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Posts by ZheFrench

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diffbind : Is it possible to analyze one sample only ?
... I have a pair of chipseq. One is really bad. Mapping failed. I was wondering if it's possible to analyse only one without the pair ?  Other question : I tried to do the analyze with both of the samples even is one is not very good. I did two different things : the first time I set the rule that ...
diffbind written 9 weeks ago by ZheFrench10 • updated 8 weeks ago by Rory Stark2.1k
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Comment: C: clusterProfiler: Which GO version is used behind ?
... By the way ,same question for Reactome ? and Kegg ? I think enrichKEGG use lastest remote version using use_internal_data=FALSE. Is there a way to upgrade these anotations  without upgrading R bioconductor. I'm stuck to R 3.3.1 and can't upgrage bioconductor withtout reinstalling a more recent vers ...
written 10 weeks ago by ZheFrench10
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Comment: C: Diffbind: dba.plot retrieve variance explained
... DiffBind_2.2.12 . It's not 3D plot.I send you that. ...
written 10 weeks ago by ZheFrench10
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clusterProfiler: Which GO version is used behind ?
... I'm using clusterProfiler v3.2.14 for GO molecular function in human.  The background size is 16309. Panther webtool give a size of 21002. Annotation Version and Release Date: GO Ontology database Released 2017-08-14 I was wondering which version of the GO database is use in ClusterProfiler. Why ...
clusterprofiler written 10 weeks ago by ZheFrench10 • updated 10 weeks ago by Guido Hooiveld2.1k
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Diffbind: dba.plot retrieve variance explained
... Is there a way to grep the percentages PC1 and PC2 variance explained from dba.plotPCA in diffbind or chipQC ? In my pca plot PC1 and PC2 numbers seem inversed . I'd like a way to recompute them from scratch (as asked here ) or to retrieve them to tcheck if they are wrongly sorted. Because from sev ...
diffbind chipqc written 12 weeks ago by ZheFrench10 • updated 9 weeks ago by Rory Stark2.1k
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Comment: C: ChIPQC : ChIPQCreport(dba_object) getting error when drawing plotFribl
... I found by myself, sorry to bother with this one, it was caused by a mistake in name of sample control inside my samplefiles.csv. Careless error :/ Sorry Thanks! ...
written 4 months ago by ZheFrench10
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ChIPQC : ChIPQCreport(dba_object) getting error when drawing plotFribl
... What is going on here ? ​ ​ ChIPQCreport(dba_chip_init,facet=T,lineBy=c("Replicate"),facetBy=c("Condition","Factor"),reportName=paste0(filename,"Marks",collapse = "_"), reportFolder=dir_output,colourBy=c("Replicate")) Saving 7 x 7 in image Saving 7 x 7 in image Saving 7 x 7 in image Error in data. ...
chipqc written 4 months ago by ZheFrench10
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Diffbind: Does Heatmap use count or score? and for which intervals ?
... Hey, I saved a first chipQC object using consensus=TRUE,bCounts=TRUE,summits=250 options. Then I reused it latter inside DiffBind. First I was wondering if it uses score or count to make heatmap ? Documentation it misleading, it is said it uses scores but if you have add also your Input, necessar ...
diffbind written 5 months ago by ZheFrench10 • updated 10 weeks ago by Rory Stark2.1k
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Comment: C: Diffbind: retrieve raw peaks per sample
... Got the following error : ​ Error in if (numCols > 0) { : argument is of length zero Calls: dba.peakset -> pv.writePeakset -> pv.do_peaks2bed UPDATE : Also tried another strategy : #' Load dba object (from ChIPQC) : dba_chip_init <- dba.load(file=filename,dir= dir_output, pre='', ...
written 5 months ago by ZheFrench10
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Diffbind: retrieve raw peaks per sample
... Trying to retrieve my raw peaks . Here trying to get peaks called by macs2 for sample L13S13 I should have 94888 but I get 269818 . Seems to be the number of consensus when taking the whole object. show(dba_chip_init) ID Tissue Factor Condition Treatment Replicate Caller Intervals 1 ...
diffbind written 5 months ago by ZheFrench10 • updated 5 months ago by Rory Stark2.1k

Latest awards to ZheFrench

Scholar 5 months ago, created an answer that has been accepted. For C: ChIPQC : ChIPQCreport(experiment) swap memory overload

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