User: Haiying.Kong

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Haiying.Kong50
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Posts by Haiying.Kong

<prev • 47 results • page 1 of 5 • next >
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Comment: C: summarizeVariants from VariantAnnotation reordering genes in rownames
... Why should they be in same order? ...
written 3 hours ago by Haiying.Kong50
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Comment: C: R Session Aborted; R ecountered a fatal error while loading openCyto
... You did not paste any error message. ...
written 3 hours ago by Haiying.Kong50
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Answer: A: Color specific genes in cummeRbund scatterplot
...   I am not familiar with this, but would this be sensible to try?   First, you need to combine all 3 kinds of gene list files, up, down, and no change. There must be one column that indicates the direction of change, and then you can translate this and get a vector colors. Then, instead of using co ...
written 3 hours ago by Haiying.Kong50
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Answer: A: Problem in merging data frames
... If you are on Windows, you can set memory limit with the function: memory.limit(size = NA) ...
written 3 days ago by Haiying.Kong50
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Comment: C: Annotation Database for ChIPpeakAnno
... Thank you very much for your reply. (1) The database TxDb.Hsapiens.UCSC.hg19.knownGene does not have gene IDs after converted to GRanges object, unless the row names, 1, 10, 100, 1000, ....... are representing gene IDs. GRanges object with 23056 ranges and 0 metadata columns:         seqnames     ...
written 3 days ago by Haiying.Kong50
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Answer: A: SomaticSignatures package : motifMatrix function trouble
... I think it is because Caf62_motifs does not have any information for sample names. So, when motifMatrix tries to sort the data by sampleNames, it cannot.   ...
written 4 days ago by Haiying.Kong50
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Annotation Database for ChIPpeakAnno
... If I use annotatePeakInBatch in ChIPpeakAnno package to annotate genomic regions with     annotatePeakInBatch(apple, AnnotationData=TSS.human.GRCh37) The annotated gene IDs are Ensembl. To be consistent with other results, I had to convert them to Hugo_Symbols, but significant amount of ENSG do ...
chippeakanno written 4 days ago by Haiying.Kong50 • updated 3 days ago by Ou, Jianhong990
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Answer: A: package "isa2", function isa.iterate()
... isa2:::isa.iterate ...
written 4 days ago by Haiying.Kong50
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Comment: C: biomaRt - Error in getBM: The query to the BioMart webservice returned an invali
... *************************************************************** It turned out to be a terrible mistake of mine: values="1" I did not read the manual carefully. *************************************************************** Hello Mike, I tried to use the package about 40 days ago. For your ref ...
written 18 days ago by Haiying.Kong50
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Comment: C: Ballgown object construction error
... i am not 100% sure. but, most likely, scan error means read error. something in your transcript data is not compatible with the function with which ballgown reads in the data. ...
written 20 days ago by Haiying.Kong50

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