User: Ngsnewbie

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Ngsnewbie360
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360
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Last seen:
4 years, 11 months ago
Joined:
8 years, 1 month ago
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a***********@gmail.com

I am working in NGS-Bioinformatics domain

Posts by Ngsnewbie

<prev • 19 results • page 1 of 2 • next >
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Comment: C: After Getting Normalization Factor Via Edger, What To Do For Normalization?
... Thanks Damian for the rectification :) ...
written 5.0 years ago by Ngsnewbie360
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After Getting Normalization Factor Via Edger, What To Do For Normalization?
... Dear All, This is a pretty simple question, but i am getting confused .. I have raw count data. I am using edgR (TMM), I got normalization factor by a function calcNormFactors in edgeR package. I got final normalized values using cpm function also. Now when i divide (also tried with multiplic ...
normalization edger written 5.0 years ago by Ngsnewbie360 • updated 5.0 years ago by Damian Kao15k
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Comment: C: Distributed Computing In Bioinformatics
... Actually I am just exploring the hadoop technology, so seeking the challenges or impact of hadoop technologies in NGS / Bioinformatics data analysis. I dont specifically want to use hadoop, but if i try with hadoop , will it be fruitful or not and what hurdles would be there? ...
written 5.5 years ago by Ngsnewbie360
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Distributed Computing In Bioinformatics
... As of now we have some Hadoop based packages (crossbow, cloudburst etc) for NGS data analysis, still I find tools like bowtie, tophat, SOAP etc that people prefer in their work. I am a biologist but still I want to get some ideas that is it possible to use / convert serial tools into map-reduce form ...
ngs written 5.5 years ago by Ngsnewbie360 • updated 5.5 years ago by Jeremy Leipzig17k
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Comment: C: How Many Replicates And Which Statistical Test Can Be Done For Preliminary Analy
... Thanks Michele Busby for such a beautiful explanation. Also, the blog post is written in a lucid way that i could able to comprehend it easily. Awesome !!! ...
written 5.6 years ago by Ngsnewbie360
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Comment: C: How Many Replicates And Which Statistical Test Can Be Done For Preliminary Analy
... Thanks Nicobxl, I can use edgeR and DESeq. Actually, While browsing through microarray data analysis, To do t-test came in my mind that will help me to understand the usage of t-test and other statistical test in gene expression analysis. The above excercise is just for learning concepts. Thus i wan ...
written 5.6 years ago by Ngsnewbie360
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How Many Replicates And Which Statistical Test Can Be Done For Preliminary Analysis With Normalized Rna-Seq Count Data?
... Before running any RNA-seq data analysis packages, I want to do statistical test for my gene expression data. I have 4 replicates for two treatment (r and s). As RNA-seq data have -ve bionomial distribution. Does it make any sense if i do gene wise paired t-test, so that i can get p-values for each ...
rnaseq gene-expression written 5.6 years ago by Ngsnewbie360 • updated 5.6 years ago by Istvan Albert ♦♦ 77k
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Comment: C: Classification Of Samples Based On Gene Expression Values
... Yes i dont know which one are which !! , and these 8 have to segregate into two groups pre-treatment and post-treatment. So the query is: I have 8 samples (of which 4 belongs to pre-treatment and 4 belongs to post treatment, but i dont know which sample belongs to which one). So i am finding out th ...
written 5.8 years ago by Ngsnewbie360
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Classification Of Samples Based On Gene Expression Values
... I have 8 samples ( of which 4 are pre treatment and 4 are post treatment ) where the sample names are unknown , means i dont know what samples belongs to pre treatment and what belongs to post treatment. The gene expression values (count value as well as FPKM) are available. So the objective is be ...
classification rna-seq clustering written 5.8 years ago by Ngsnewbie360 • updated 5.1 years ago by Biostar ♦♦ 20
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Comment: C: Could Biostar Have Polls Or Rating Systems For Analysis Tools Or Databases
... I hope biostar will come up with some lucrative and relevant feature :) ...
written 6.0 years ago by Ngsnewbie360

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