User: rice.researcher

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Korea, Republic Of
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Posts by rice.researcher

<prev • 8 results • page 1 of 1 • next >
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Comment: C: How to plot Z-scores in R for gene expression data
... Even without clustering, you can generate such image. For ex, in the left panel of MeV, go to Cluster manager->Gene clusters. Then you can find a drop down box (at left top) and select expression graph option. ...
written 13 days ago by rice.researcher60
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Answer: A: How to plot Z-scores in R for gene expression data
... You can use free software MultiExperiment Viewer (MeV) for generating the plot mentioned in the article. Documentation is available [Here][1] [1]: https://www.decodon.com/files/doc/MeV_Manual_4_0.pdf ...
written 13 days ago by rice.researcher60
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Comment: C: For only a few genes, Cuffdiff report more than one FPKM values per locus. Why?
... Thanks for the direction@theobroma22 ...
written 6 months ago by rice.researcher60
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Comment: C: For only a few genes, Cuffdiff report more than one FPKM values per locus. Why?
... Processor failing could result in such fragmentation?Any previous experience? BTW I noticed that using similar commands with this annotation file gave me unfragmented FPKM previously, means its not a problem with annotation file @theobromma22 ...
written 6 months ago by rice.researcher60
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For only a few genes, Cuffdiff report more than one FPKM values per locus. Why?
... I followed similar steps mentioned in the procedure part of [Trapnell et al, 2012][1] for an RNASeq analysis of oryza sativa datasets. The problem I face is in the Cuffdiff output, where more that one FPKM value is reported for many genes as below, test_id gene_id gene locus sample_1 ...
cufflinks tophat degs cuffdiff rna-seq written 6 months ago by rice.researcher60 • updated 6 months ago by theobroma22930
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Method for enrichment analysis for the QTL terms
... I have a micro-array anatomical tissue based co-expressed list of around 80 genes. For each of this gene, I found out the QTL terms associated with it from a genome wide QTL mapped to gene in the organism. For every gene, there are multiple QTL term similar to GO assignment. I would like to know wh ...
qtl gene ontology written 18 months ago by rice.researcher60
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Comment: C: Plotting and Visualizing large number of genes into chromsome
... I thought there might be some tools which provide a scattered plot kind of mapping ( I mean many dots) onto chromosome. My  list is having 3450 genes. In this case, I am not using connector to link genes@Devon Ryan  ...
written 2.5 years ago by rice.researcher60
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Plotting and Visualizing large number of genes into chromsome
... Hello.... I have a list of arounfd 5000 rice genes. I would like to display those genes in rice chromosome. I tried with Rcircos, tool is good but it can map upto a few genes. So I am in trouble.!! I know about circos but it is beyond my limit to execute. Do anyone of you have an idea about method/ ...
rice visualization rcircos chromosome written 2.5 years ago by rice.researcher60 • updated 7 months ago by bernatgel770

Latest awards to rice.researcher

Scholar 13 days ago, created an answer that has been accepted. For A: How to plot Z-scores in R for gene expression data
Teacher 13 days ago, created an answer with at least 3 up-votes. For A: How to plot Z-scores in R for gene expression data
Popular Question 16 months ago, created a question with more than 1,000 views. For Plotting and Visualizing large number of genes into chromsome

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