Moderator: Jean-Karim Heriche

Reputation:
9,860
Status:
Trusted
Location:
EMBL Heidelberg, Germany
Website:
http://jkh1.github.io/
Last seen:
31 minutes ago
Joined:
5 years, 10 months ago
Email:
h******@embl.de

Posts by Jean-Karim Heriche

<prev • 1,239 results • page 1 of 124 • next >
0
votes
2
answers
68
views
2
answers
Comment: C: Calculating p-Value for an observed/expected Ratio
... You can do the permutation test after you have processed the data. ...
written 31 minutes ago by Jean-Karim Heriche9.9k
1
vote
2
answers
68
views
2
answers
Answer: A: Calculating p-Value for an observed/expected Ratio
... This looks like a permutation test. Your p-value would be the number of times the permutations give more reads mapping to the feature under consideration divided by the number of permutations. And if you're doing multiple tests (i.e. testing many features), you should do a correction for multiple t ...
written 2 hours ago by Jean-Karim Heriche9.9k
0
votes
1
answer
81
views
1
answers
Comment: C: how the duplicated interactions looks like in HPRD data ?
... IRefIndex is a compilation of several protein-protein interaction databases and so includes human data. Read the [paper][1] to understand how it's done. To get human data only, just filter on the taxon ID in the relevant columns. So if you need to look for interactions involving genes in your lists ...
written 2 hours ago by Jean-Karim Heriche9.9k
0
votes
1
answer
60
views
1
answers
Comment: C: Improve Large Heatmap Generation in R
... Think about what you want to show. What's the message of the figure ? There's no point having a heatmap (or any other type of figure for that matter) that can't be legibly displayed on standard media (e.g. computer screen or paper). First, if the problem is that there are no patterns to be seen wher ...
written 3 hours ago by Jean-Karim Heriche9.9k
0
votes
4
answers
76
views
4
answers
Comment: C: Compare pairs of key/value of perl hash tables
... Just because you mention sets, I'll also mention the [Set::Scalar][1] module. [1]: http://search.cpan.org/~davido/Set-Scalar-1.29/lib/Set/Scalar.pm ...
written 3 hours ago by Jean-Karim Heriche9.9k
3
votes
4
answers
76
views
4
answers
Answer: A: Compare pairs of key/value of perl hash tables
... You're looking for lines that are common between two files. Ther are plenty of solutions on the net already. You could use [comm][1] command or if you want to use perl and both files fit in memory, you can read then into arrays and use [List::Compare][2]. [1]: http://pubs.opengroup.org/onlinepub ...
written 14 hours ago by Jean-Karim Heriche9.9k
0
votes
0
answers
68
views
0
answers
Comment: C: clustering cell population in different phenotypes
... So if I understand correctly, you have a 48 rows (samples) x 4 columns (genes) data matrix and you want to cluster the rows into 5 clusters. Depending on what you believe (or assumptions you can make) about the replicates, you can combine them into one vector either by averaging or by taking the med ...
written 19 hours ago by Jean-Karim Heriche9.9k
1
vote
2
answers
120
views
2
answers
Comment: C: Explain Forward algorithm for Hidden Markov Model
... Sounds too much like homework. Post your solution and we'll check it. ...
written 1 day ago by Jean-Karim Heriche9.9k
4
votes
2
answers
97
views
2
answers
Answer: A: Does BioMart based go-terms contain any insignificant go-terms ?
... BioMart doesn't perform any analysis. It simply gives access to the annotations, i.e when you query BioMart with a list of genes to get GO terms, it returns all the GO terms the query genes have been annotated with. ...
written 1 day ago by Jean-Karim Heriche9.9k
0
votes
1
answer
84
views
1
answers
Answer: A: kNN algorithm on microarray data - training labels definition
... You're not telling us what you're using but I assume this is the knn() function from the R package class. If so cl should get a factor with one entry for each instance of the training set, i.e. in your case train_labels should be a factor of length 70. ...
written 1 day ago by Jean-Karim Heriche9.9k

Latest awards to Jean-Karim Heriche

Teacher 3 hours ago, created an answer with at least 3 up-votes. For A: Rnai Screening Data Repositories?
Teacher 1 day ago, created an answer with at least 3 up-votes. For A: Rnai Screening Data Repositories?
Scholar 1 day ago, created an answer that has been accepted. For A: Bonferonni Correction for mostly overlapping enhancers
Teacher 3 days ago, created an answer with at least 3 up-votes. For A: Rnai Screening Data Repositories?
Scholar 6 days ago, created an answer that has been accepted. For A: Bonferonni Correction for mostly overlapping enhancers
Teacher 8 days ago, created an answer with at least 3 up-votes. For A: Rnai Screening Data Repositories?
Appreciated 19 days ago, created a post with more than 5 votes. For C: What is a gene transcript?
Good Answer 19 days ago, created an answer that was upvoted at least 5 times. For A: Normalized Smith-Waterman Formula
Teacher 19 days ago, created an answer with at least 3 up-votes. For A: Rnai Screening Data Repositories?
Scholar 19 days ago, created an answer that has been accepted. For A: Bonferonni Correction for mostly overlapping enhancers
Teacher 28 days ago, created an answer with at least 3 up-votes. For A: Rnai Screening Data Repositories?
Scholar 28 days ago, created an answer that has been accepted. For A: Bonferonni Correction for mostly overlapping enhancers
Teacher 29 days ago, created an answer with at least 3 up-votes. For A: Rnai Screening Data Repositories?
Scholar 29 days ago, created an answer that has been accepted. For A: Bonferonni Correction for mostly overlapping enhancers
Scholar 5 weeks ago, created an answer that has been accepted. For A: Bonferonni Correction for mostly overlapping enhancers
Teacher 5 weeks ago, created an answer with at least 3 up-votes. For A: Rnai Screening Data Repositories?
Scholar 7 weeks ago, created an answer that has been accepted. For A: Bonferonni Correction for mostly overlapping enhancers
Teacher 7 weeks ago, created an answer with at least 3 up-votes. For A: Rnai Screening Data Repositories?
Commentator 7 weeks ago, created a comment with at least 3 up-votes. For C: Principal component analyses
Teacher 7 weeks ago, created an answer with at least 3 up-votes. For A: Rnai Screening Data Repositories?
Scholar 7 weeks ago, created an answer that has been accepted. For A: GO term enrichment
Good Answer 7 weeks ago, created an answer that was upvoted at least 5 times. For A: Normalized Smith-Waterman Formula
Scholar 7 weeks ago, created an answer that has been accepted. For A: Bonferonni Correction for mostly overlapping enhancers
Scholar 7 weeks ago, created an answer that has been accepted. For A: Bonferonni Correction for mostly overlapping enhancers

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1298 users visited in the last hour