User: arronar

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arronar50
Reputation:
50
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New User
Location:
Austria
Last seen:
1 month, 4 weeks ago
Joined:
3 years, 2 months ago
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3************@gmail.com

Posts by arronar

<prev • 79 results • page 1 of 8 • next >
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Is the application of Decision Trees proper algorithm for micro arrays data ?
... Hello out there. I was thinking to apply decision tree algorithm on my microarrays data as a supervised method for learning but all examples found out there are using binary categorical variable. Either alive or dead, either red or green, either sun or rain and so on. That realization made me wonde ...
R microarray decision tree written 8 weeks ago by arronar50
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Comment: C: Calculating variable importance in model for microarray dataset
... If i understood after the colMeans() I'm going to have a new matrix with 6 (treatments) x 920 (genes). Isn't this matrix too small to get training and test data from it ? To train the kNN i need at least one occasion from each treatment. That means that I will use all 6 rows to train the algorithm. ...
written 8 weeks ago by arronar50
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Comment: C: Calculating variable importance in model for microarray dataset
... To be honest I didn't exactly understood what you just said :-) ...
written 8 weeks ago by arronar50
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Comment: C: Calculating variable importance in model for microarray dataset
... Bad news. It has 80% error with k=31. Here is the image. ![enter image description here][1] Also, Ii just see a mistake that I made in my initial post. I didn't mean 30-35%. I meant 50-55% error rate. 30-35% I can get only if i delete some of the replication treatments that has low correlation in ...
written 8 weeks ago by arronar50
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Comment: C: Calculating variable importance in model for microarray dataset
... Hi theobroma22 My Initial matrix is 920x60. I used the 70% of this as training set and the rest 30% as test set. I did this 100 different times using sample() function and for k number 1:20. While the error rate i counted as below: for(y in 1:100){ train_set = sample(...) t ...
written 8 weeks ago by arronar50
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Calculating variable importance in model for microarray dataset
... Hi. I'm analyzing a microarray dataset that is consisted by 920 variables (genes) and 6 samples (treatments) with replications (10 replications per sample) I ran a kNN classification on those data with knn() function in R for 100 different samples each time and I got an error rate about 30-35%. S ...
R modeling microarray knn r language written 8 weeks ago by arronar50
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kNN algorithm on microarray data - training labels definition
... Hello. I have a bunch of migroarray data in an array and i wanna run the kNN algorithm on them. So for simplicity let's say that I have for 100 genes in 4 different treatments a table with expression levels. | Gene name | Treat 1 | Treat 2 | Treat 3 | Treat 4| ----------------------------- ...
R microarray knn written 9 weeks ago by arronar50 • updated 9 weeks ago by Jean-Karim Heriche12k
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Comment: C: Widening the distances between PCA vectors in PCA a biplot
... Thank you very much. Seems that it works. ...
written 11 weeks ago by arronar50
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Widening the distances between PCA vectors in PCA a biplot
... Hello. I'm running a PCA analysis on R with 62 variables and when creating the biplot some vectors are getting on top of others and i cannot read their labels (see pic). Is there any way to make them more readable. ![enter image description here][1] I used the factoextra package to plot it by ru ...
bioplot R piblot pca vector written 11 weeks ago by arronar50 • updated 11 days ago by Alex Reynolds19k
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Comment: C: PCA for deregulated genes - technical question
... The initial microarray data was expression values and normalized them with quantile method. Then i run on them a dunnet's test to get the most significant deregulated (differentially expressed) genes. Let's say that for each treatment i got the following DE genes deregulated_treat1 = c( 1, 2, 3 ...
written 12 weeks ago by arronar50

Latest awards to arronar

Popular Question 9 weeks ago, created a question with more than 1,000 views. For "found spliced alignment without XS attribute" while running cuffmerge
Popular Question 9 weeks ago, created a question with more than 1,000 views. For "found spliced alignment without XS attribute" while running cuffmerge
Popular Question 11 weeks ago, created a question with more than 1,000 views. For "found spliced alignment without XS attribute" while running cuffmerge
Supporter 3 months ago, voted at least 25 times.
Popular Question 7 months ago, created a question with more than 1,000 views. For "found spliced alignment without XS attribute" while running cuffmerge
Popular Question 13 months ago, created a question with more than 1,000 views. For Problem using a custom blast database in tblastx
Popular Question 2.3 years ago, created a question with more than 1,000 views. For Problem using a custom blast database in tblastx
Popular Question 2.3 years ago, created a question with more than 1,000 views. For data from SRA against blast databases method.

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