User: ZheFrench
ZheFrench • 10
- Reputation:
- 10
- Status:
- New User
- Location:
- Last seen:
- 1 week, 1 day ago
- Joined:
- 1 year, 6 months ago
- Email:
- j*********@gmail.com
Posts by ZheFrench
<prev
• 44 results •
page 1 of 5 •
next >
0
votes
0
answers
64
views
0
answers
... 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 ...
written 8 weeks ago by
ZheFrench • 10
2
votes
1
answer
179
views
1
answer
... 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
...
written 4 months ago by
ZheFrench • 10
• updated 4 months ago by
Alejandro Reyes • 1.5k
0
votes
0
answers
156
views
0
answers
... 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 ...
written 5 months ago by
ZheFrench • 10
0
votes
1
answer
197
views
1
answer
... 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 ...
written 7 months ago by
ZheFrench • 10
• updated 7 months ago by
Rory Stark • 2.4k
0
votes
1
answers
361
views
1
answers
... 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 7 months ago by
ZheFrench • 10
0
votes
2
answers
537
views
2
answers
... DiffBind_2.2.12 . It's not 3D plot.I send you that.
...
written 7 months ago by
ZheFrench • 10
2
votes
1
answer
361
views
1
answer
... 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 ...
written 7 months ago by
ZheFrench • 10
• updated 7 months ago by
Guido Hooiveld • 2.2k
2
votes
2
answers
537
views
2
answers
... 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 ...
written 7 months ago by
ZheFrench • 10
• updated 7 months ago by
Rory Stark • 2.4k
0
votes
0
answers
179
views
0
answers
... 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 9 months ago by
ZheFrench • 10
1
vote
0
answers
179
views
0
answers
...
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. ...
written 9 months ago by
ZheFrench • 10
Latest awards to ZheFrench
Scholar
10 months ago,
created an answer that has been accepted.
For C: ChIPQC : ChIPQCreport(experiment) swap memory overload
Use of this site constitutes acceptance of our User
Agreement
and Privacy
Policy.
Powered by Biostar
version 2.2.0
Traffic: 178 users visited in the last hour