User: ZheFrench

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ZheFrench10
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2 months, 2 weeks ago
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1 year, 9 months ago
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Posts by ZheFrench

<prev • 44 results • page 1 of 5 • next >
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ChIPQC : ChIPQCreport : Error: Dimensions exceed 50 inches when saving plot with large sampleSheet
... Trying to plot report  ChIPQCreport with a sampleSheet containing 60 samples I get the following error. Error: Dimensions exceed 50 inches (height and width are specified in 'in' not pixels). If you're sure you want a plot that big, use `limitsize = FALSE`. CCPlot.png and CoverageHistogramPlot.pn ...
chipqc written 4 months ago by ZheFrench10
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DEXSeqHTML and biomart object
... Could you provide a more detailed example of code to use biomart object and extra columns to add for example GeneSymbol in the output of DEXSeqHTML  ? Not clear to me how you use mart  and attributes parameters in DEXSeqHTML   ...
dexseq written 7 months ago by ZheFrench10 • updated 7 months ago by Alejandro Reyes1.6k
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DEXSeq : Preprocessing within R for Forward-Reverse Library
... I'm treating RNA-SEQ with forward-reverse library. In the doc part 2.5 you explained very well how to configure Strandedness using the python script and the -s reverse option..(as htseqcount...) In part B of the tutorial,  Preprocessing within R , it's not clear to me how you configure that only u ...
dexseq written 7 months ago by ZheFrench10
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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 10 months ago by ZheFrench10 • updated 9 months ago by Rory Stark2.5k
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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 months 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 months 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 months ago by ZheFrench10 • updated 10 months ago by Guido Hooiveld2.3k
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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 10 months ago by ZheFrench10 • updated 10 months ago by Rory Stark2.5k
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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 12 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 12 months ago by ZheFrench10

Latest awards to ZheFrench

Scholar 13 months ago, created an answer that has been accepted. For C: ChIPQC : ChIPQCreport(experiment) swap memory overload

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