User: NetunoPoncã

gravatar for NetunoPoncã
NetunoPoncã160
Reputation:
160
Status:
Trusted
Location:
Brazil
Last seen:
1 year, 8 months ago
Joined:
7 years ago
Email:
p**********@gmail.com

Posts by NetunoPoncã

<prev • 20 results • page 1 of 2 • next >
2
votes
1
answer
1.3k
views
1
answers
Answer: A: How to implement neural networks?
... You are talking about classification, that is, inducing a model based on trainning data in order to classify (predict the labels) of previsously unseen data. Neural networks are just one possibility. If you want to implement them from scratch, I suggest you take a look here: - Neural Networks and L ...
written 4.2 years ago by NetunoPoncã160
1
vote
2
answers
906
views
2
answers
RNA-Seq Introductory Material
... Hello, I used to work with microarray data. When I was begining in the field I found several good and introductory reviews that helped a lot for someone with computer science background. For instance: 1. Alvis Brazma, Jaak Vilo, Gene expression data analysis, FEBS Letters, Volume 480, Issue 1, 25 ...
rna-seq written 4.2 years ago by NetunoPoncã160 • updated 4.2 years ago by Charles Warden7.3k
0
votes
3
answers
19k
views
3
answers
Comment: C: TCGA RNA-Seq Data: RSEM and RPKM
... I already saw that page, but thanks for citing it. I realize that they do not provide RPKM values per gene, but I guessed it would be "easy" to derive these values from other information available in the files... I guess it is not the case. ...
written 5.0 years ago by NetunoPoncã160
0
votes
3
answers
19k
views
3
answers
Comment: C: TCGA RNA-Seq Data: RSEM and RPKM
... Hi, I can find this for RNASeqV1 data, but not for RNASeqV2 data. Any ideas? Furthermore, only a couple of data have this available for RNASeqV1 data... Is it possible to obtain this for RNASeqV2 data? ...
written 5.0 years ago by NetunoPoncã160
14
votes
3
answers
19k
views
5 follow
3
answers
TCGA RNA-Seq Data: RSEM and RPKM
... Hi there, I am currently using TCGA-Assembler to download TCGA data. I am interested in the RPKM and RSEM values for each gene. For RSEM i can easily obtain the values per gene (around 20k values per sample). For RPKM, on the other hand, I can only obtain values regarding each exon (around 230k val ...
rpkm tcga rsem tcga-assembler rna-seq written 5.0 years ago by NetunoPoncã160 • updated 3.1 years ago by Biostar ♦♦ 20
0
votes
1
answer
1.2k
views
1
answers
Answer: A: microarray data set
... If you need "ready" preprocessed data, this study will probably help: http://www.biomedcentral.com/1471-2105/9/497 Cheers. ...
written 5.1 years ago by NetunoPoncã160
1
vote
1
answer
2.2k
views
1
answers
Answer: A: pairwise distance in phylogeny tree in matlab
... Hi there, as i understand the plot is correct. As matlab specifies, in your distance vector you have the distance between: [ (Leaf 2, Leaf 1); (Leaf 3, Leaf 1); (Leaf 3, Leaf 2) ] = [10, 10, 4] (help seqpdist). If you take a look at the dendrogram, it displays the highest distance at the bottom ( ...
written 5.1 years ago by NetunoPoncã160
0
votes
3
answers
2.3k
views
3
answers
Comment: C: question about clustering of samples
... Ok, now i got it. That's an option, i guess. If you are going to run k-means, be sure to run it multiple times and select as final solution the one with minimum error (sse) - only if you run it for the same number of clusters (sse decreases with more clusters), as i understand you are going to do. G ...
written 5.4 years ago by NetunoPoncã160
0
votes
3
answers
2.3k
views
3
answers
Comment: C: question about clustering of samples
... yeah, your cluster 3 is weird (for the class labels you are setting)... any chance of measuring error? Moreover, k-means is not deterministic, how many runs have you tried? I'm not familiar with the problem (i'm familiar with clustering, not your particular application), but, is any other class stru ...
written 5.4 years ago by NetunoPoncã160
1
vote
2
answers
1.6k
views
2
answers
Answer: A: How To Find The Distance Between Genes After Performing A Clustering
... What do you mean by the distance between genes? The distance between them is the same before or after clustering, unless you use a measure of distance between clusters! If you want the distance between genes, simply compute it with the desired measure... their distance is not going to change after ...
written 5.4 years ago by NetunoPoncã160

Latest awards to NetunoPoncã

Appreciated 2.8 years ago, created a post with more than 5 votes. For TCGA RNA-Seq Data: RSEM and RPKM
Good Question 2.8 years ago, asked a question that was upvoted at least 5 times. For TCGA RNA-Seq Data: RSEM and RPKM
Epic Question 3.0 years ago, created a question with more than 10,000 views. For TCGA RNA-Seq Data: RSEM and RPKM
Student 3.6 years ago, asked a question with at least 3 up-votes. For Find Kegg Pathway That Contain Certain Genes
Great Question 4.1 years ago, created a question with more than 5,000 views. For TCGA RNA-Seq Data: RSEM and RPKM
Popular Question 4.1 years ago, created a question with more than 1,000 views. For Processed RNA-SEQ Datasets
Popular Question 4.1 years ago, created a question with more than 1,000 views. For TCGA RNA-Seq Data: RSEM and RPKM
Popular Question 4.2 years ago, created a question with more than 1,000 views. For Find Kegg Pathway That Contain Certain Genes
Popular Question 4.7 years ago, created a question with more than 1,000 views. For TCGA RNA-Seq Data: RSEM and RPKM
Student 5.5 years ago, asked a question with at least 3 up-votes. For Find Kegg Pathway That Contain Certain Genes

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1704 users visited in the last hour