User: zhilongjia

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zhilongjia0
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2 years, 11 months ago
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Posts by zhilongjia

<prev • 8 results • page 1 of 1 • next >
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Answer: A: a question about getCdfInfo package in GCRMA, thanks for your help.
... Adding mydata@cdfName <- "U133_X3P" before eset_gcrma<-gcrma(mydata) will work. ...
written 24 months ago by zhilongjia0
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Comment: C: AnnotationForge failed due to "Parameter 0 does not have length 1"
... Sent. Thank you. ...
written 2.0 years ago by zhilongjia0
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AnnotationForge failed due to "Parameter 0 does not have length 1"
... I used AnnotationForge to build an annotation package. And when I use makeDBPackage function, it does not work as printing "Error: Parameter 0 does not have length 1." Error: Parameter 0 does not have length 1. 12 stop(structure(list(message = "Parameter 0 does not have length 1.", call = NU ...
annotationforge written 2.0 years ago by zhilongjia0 • updated 2.0 years ago by Valerie Obenchain ♦♦ 6.4k
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Comment: C: Common workflow to build an microarray annatation package, like hgu133a.db
... About AnnotationForge, Here I have the probe name and sequence (for example, for GPL6480). I do not want to use the annotation from GEO and want to update the annotation by myself. However, AnnotationForge requires a kind of id (such as Genbank ID) with the probe name. Here it seems mapping is the f ...
written 2.0 years ago by zhilongjia0
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Comment: C: Common workflow to build an microarray annatation package, like hgu133a.db
... Thank you for your remind. Here I want to know the common workflow to build this kind of annotation package and HUG133a is an example. ...
written 2.0 years ago by zhilongjia0
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Comment: C: Common workflow to build an microarray annatation package, like hgu133a.db
... ReadAffy(), working with Affymetrix only, will return an AffyBatch object with an annotation name, such as hgu133plus2, by function annotation(). And the featureData will be null (Why it's null? which means it does not catch the annotation package information automatically). While if getGEO() is use ...
written 2.0 years ago by zhilongjia0
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Comment: C: Common workflow to build an microarray annatation package, like hgu133a.db
... Thank you. I will check AnnotationForge package. About the naming, another example is hgug4112a to Agilent-012391 Whole Human Genome Oligo Microarray G4112A (Feature Number version). It's awkward to find the mapping relationship between them if there is no the gist file supplied by seandavi, which ...
written 2.0 years ago by zhilongjia0
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Common workflow to build an microarray annatation package, like hgu133a.db
... What is the common work-flow to build an microarray annotation package, like hgu133a.db.   For some array, there are probe sequences available, then maybe mapping is used? While for other situations, how to deal with? If code used by the team available, that will be great. Thank you. The specific ...
annotation written 2.0 years ago by zhilongjia0 • updated 2.0 years ago by James W. MacDonald45k

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