User: hanguangchun

gravatar for hanguangchun
hanguangchun120
Reputation:
120
Status:
Trusted
Location:
United States
Last seen:
10 months, 4 weeks ago
Joined:
5 years, 2 months ago
Email:
h***********@gmail.com

about me

Posts by hanguangchun

<prev • 60 results • page 1 of 6 • next >
0
votes
3
answers
14k
views
3
answers
Answer: A: Guide to TCGA data
... great summary for those who are unfamiliar with how to fetch the data ...
written 18 months ago by hanguangchun120
0
votes
1
answer
753
views
1
answers
Comment: C: low expressed gene filtration, quantile normalization and log2 transformation, w
... Thank you. exactly, for raw read count of rna-seq data, I usually use deseq2 and edger to do DEG analysis. but sometimes I have to go with only rpkm/fpkm data. that's where I get trouble. ...
written 19 months ago by hanguangchun120
0
votes
1
answer
753
views
1
answers
Comment: C: low expressed gene filtration, quantile normalization and log2 transformation, w
... Thank you very much for the information, Farbod. ...
written 19 months ago by hanguangchun120
0
votes
1
answer
753
views
1
answers
Comment: C: low expressed gene filtration, quantile normalization and log2 transformation, w
... Hi WouterDeCoster, I want to make it as general for both RNA-seq and microarray. ...
written 19 months ago by hanguangchun120
0
votes
1
answer
753
views
1
answer
low expressed gene filtration, quantile normalization and log2 transformation, which one goes first?
... Hi everyone, I have been dealing with expression data for about 4 years (both microarray and rna-seq). but this question still confuses me when I do data preprocessing. 1) My opinion is that at least we should do low expressed gene filtration first. Reason is that: the aim for quantile/log2 transfo ...
quantile preprocessing log2 data transform written 19 months ago by hanguangchun120 • updated 19 months ago by Farbod3.1k
0
votes
1
answer
613
views
1
answers
Comment: C: limma applied to unbalanced micro-array experiment
... Hi Devon Ryan. thank you for your reply. Since I have only one sample as control, will limma handle this kind of situiation properly? ...
written 20 months ago by hanguangchun120
0
votes
1
answer
613
views
1
answer
limma applied to unbalanced micro-array experiment
... Hello, I have a microarray gene expression dataset which consists of 5 treated samples and only 1 control samples. I know that this kind of unbalanced design is not good for differential gene expression analysis. what I want to know is that which kind of differential gene expression method is most ...
unbalanced design limma differential expression written 20 months ago by hanguangchun120 • updated 20 months ago by Devon Ryan80k
0
votes
4
answers
13k
views
4
answers
Answer: A: Where Can I Get The Asperasoft Command Line Client Ascp
... the ascp binary will be installed in $ASPERA_ROOT/connect/bin/(/home/.aspera/connect/bin for linux) when you install aspera connect plugin. ...
written 2.9 years ago by hanguangchun120
0
votes
1
answer
1.0k
views
1
answer
Solid RNA-seq pair end alignment read orientation
... Hi all, recently I have mapped a SOLiD 5500xl pair end sequencing data to reference transcripts. Only uniquely mapped reads are retained. after imported to intergretive genome viewer, I found that the read orientation is un-identical to the IGV doucumentation  which says that for SOLiD data, it is ...
solid rna-seq orientation written 2.9 years ago by hanguangchun120 • updated 2.9 years ago by Brian Bushnell15k
0
votes
1
answer
962
views
1
answers
Comment: C: microarray data processing
... thanks for your reply, Devon Ryan. I think you mean that those 100 genes randomly selected can represent the whole ~20000genes. that is reasonable. but it is not always the case. I have try the code in this post for other independent data sets, there are cases that it show no correlation at all. Ac ...
written 2.9 years ago by hanguangchun120

Latest awards to hanguangchun

Popular Question 13 months ago, created a question with more than 1,000 views. For Where To Get The Annotation File For The Nimblegen Seqcap Ez Exome V1
Popular Question 13 months ago, created a question with more than 1,000 views. For Protein Sequence Homology Score, Align Or Blast
Popular Question 20 months ago, created a question with more than 1,000 views. For Protein Sequence Homology Score, Align Or Blast
Popular Question 2.5 years ago, created a question with more than 1,000 views. For Protein Sequence Homology Score, Align Or Blast
Popular Question 2.5 years ago, created a question with more than 1,000 views. For Where To Get The Annotation File For The Nimblegen Seqcap Ez Exome V1
Popular Question 2.5 years ago, created a question with more than 1,000 views. For Variant Annotation Integrator From Ucsc
Popular Question 2.5 years ago, created a question with more than 1,000 views. For How To Perform A Pathway Or Network Level Analysis Of Rare Variants?
Popular Question 3.6 years ago, created a question with more than 1,000 views. For Bedtools Multicov Need A Bam Index File Specification Option

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1047 users visited in the last hour