User: rice.researcher

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Posts by rice.researcher

<prev • 21 results • page 1 of 3 • next >
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Comment: C: multiple sequence alignment
... [mauve][1] and [VISTA][2]can be used to align genomes and to analyze synthetic regions. [1]: http://darlinglab.org/mauve/mauve.html [2]: http://genome.lbl.gov/vista/index.shtml ...
written 7 days ago by rice.researcher80
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Comment: C: Tools for viral metagenomics profiling and abundance estimation using BAM file
... Ok I got it, thanks!! ...
written 9 days ago by rice.researcher80
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Comment: C: Looking for publicly available dataset.
... [ArrayExpress][1] has number of processed data and filtering option may show dataset you are looking for. [1]: https://www.ebi.ac.uk/arrayexpress/browse.html ...
written 10 days ago by rice.researcher80
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Comment: C: cuffdiff error "number of labels must match number of conditions"
... Previously I also faced this problem and a [solution][1] given in this thread by Devon Ryan solved it. [1]: https://www.biostars.org/p/129622/ ...
written 10 days ago by rice.researcher80
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Comment: C: How to integrate multiple data sets from microarray platform prior meta-analysis
... Very well explained !!. I am looking into it. ...
written 10 days ago by rice.researcher80
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Comment: C: How to integrate multiple data sets from microarray platform prior meta-analysis
... Thanks for your views and suggestion. Affymetrix array are of different platforms with different experimental design. But I am not into DE and enrichment analysis other than data integration.Yes, those R packages are new to me and I would use it for comparison. ...
written 11 days ago by rice.researcher80
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Comment: C: How to integrate multiple data sets from microarray platform prior meta-analysis
... Thanks for your suggestion!. My Affymetrix data sets are from different version and I tried the second choice. I already normalized all data sets separately and got the intensity values. Data sets were merged based on common probes. But I couldn't understand the last point as my statistical experi ...
written 11 days ago by rice.researcher80
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How to integrate multiple data sets from microarray platform prior meta-analysis?
... Efficient method(s) for comparison of data sets that are generated from different microarray experiments (meta-analysis) have been asked [previously][1]. Based on the discussion, I found [RankProd][2] R package. However, after using the method, I wanted to compare the results with an another method ...
R microaray meta-analysis microarraay written 12 days ago by rice.researcher80 • updated 11 days ago by svlachavas300
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Comment: C: Tools for viral metagenomics profiling and abundance estimation using BAM file
... Sorry,I forgot to mention that my samples are from specific environments (like saline condition and sea sediments) and not based on a host like human. I check both tools, DisCVR: It is mentioned that currently, the pipeline is suitable for human viruses. So its not an option in my case. So, I dec ...
written 14 days ago by rice.researcher80
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Tools for viral metagenomics profiling and abundance estimation using BAM file
... My aim is to perform **taxonomic classification and transcript abundance estimation** of **viral** communities from metagenomics sequenced reads. As the first step, I mapped all the reads to a reference which was built (bowtie2-built) based on refseq [viral genomes][1]. Currently, I have SAM and BAM ...
viral profiling metagenomics ngs written 14 days ago by rice.researcher80

Latest awards to rice.researcher

Scholar 11 weeks ago, created an answer that has been accepted. For A: How to plot Z-scores in R for gene expression data
Teacher 11 weeks 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 18 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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