If you have a small dataset and you want to put it into visualization and shared on the web, the most handy way is the Google chart api. Although the data requests are via http get so you probably can't visualize thousands of data points, but it's very handy to make simple plots to work, in a realtime manner.
And everyone can make up to 250,000 calls per day! Wow! Which means you can do some really cool web data services. This is not entirely new, actually some libs like Ext they do have extension gadgets specifically aimed at Google Charts.
Nevertheless, it took me like only 40 min to read the API and added a little working hours tracking gadget on this blog. It's actually dynamic; i will add some navigation buttons later. It's just another incentive to keep reminding myself do not waste time on forums, and concentrate on the work =)
Google Chart Link
Thursday, March 26, 2009
Tuesday, March 24, 2009
R libraries [Clustering, Classification, LM]
Nice functions to quickly manipulate Rmetrics: fUtilities package
Basic libs:
cluster
class
stat
Model based:
mclust
Linear Models:
MASS
lmtest
car
This post will be updated.
Basic libs:
cluster
class
stat
Model based:
mclust
Linear Models:
MASS
lmtest
car
This post will be updated.
Monday, March 23, 2009
WGCNA Package
A package for weighted correlation network analysis. It would be interesting to look at how this method can do for network analysis.
Resource Link
Paper Link
Resource Link
Paper Link
GeneNet Package
To do data transformations, there's a package named GeneNet; designed to analyze gene expression (time series) with the focus on gene networks.
they have handy transformation functions:
z.transform and hotelling.transform.
Note that these two transformations only work on correlation coefficients, with the range from -1 to 1.
Link
they have handy transformation functions:
z.transform and hotelling.transform.
Note that these two transformations only work on correlation coefficients, with the range from -1 to 1.
Link
Sunday, March 22, 2009
Bagged Clustering
A given partitioning clustering algorithm is run repeatedly on bootstrapped data, the cluster centers then merged by hierarchical cluster algorithm. This is good for noisy data / small sample size.
From R library e1071, function bclust
R Doc Link
Also here's an online powerpoint that demonstrates the application on simulated metabolomics data:
Bagged K-means Metabolomics PPT
From R library e1071, function bclust
R Doc Link
Also here's an online powerpoint that demonstrates the application on simulated metabolomics data:
Bagged K-means Metabolomics PPT
Tuesday, February 10, 2009
Thursday, January 8, 2009
Vista 64 = Messy Awesomeness
It took me a whole day to back up and install windows vista 64. Finally i can access my 8G of ram. Some softwares are heavily ram chewers (The gigantic adobe bundles) so even 3.25G ram is kinda skinny now.
Here are some of the issues:
1. Some OEM vista cdkeys are interchanageable for 32 bit and 64 bit versions. I have tried my ultimate 32 bit vista key and it works gracefully with the 64 bit DVD.
2. Cheap stuff = bad compatibility. The wireless dongle i bought for 15 bucks now shows the weakness over a pci wireless card: no driver for vista 64. I have to hook up two 3 meter cable to reach the router, and i still have the plastic connector back 3 years ago. And it rocks!
3. Weird file protection issues. Ok, here's what it is. Some softwares like acrobat reader will create some protection over certain files even admin can't delete in the first few tries. You need to 'takeover' the file ownership then 'grant' it to new administrators. Luckily these commands supports *.* batches...otherwise i have to manually deal with hundreds of files.
If you got access denied:
takeown /f file_name
icacls file_name /grant administrators:F
Then you may delete all the files.
There may be a hidden manual that can turn the entire vista into commandline?
4. There was a weird *.mov file on my computer in vista 32 that i could not remove before. First i thought it was related to hardware failure (NOOOO!) Chkdsk was totally green. I can play this file, it was fine, but any other operations, like rename, cut, delete, even right click on properties will freeze the explorer. I turned off OAS still no luck. Some googling showed that ppl have encountered similar issues, but no clear solutions were provided. Besides, this was not related to privileges.
Now i will see how vista works with my 8G of ram.
Here are some of the issues:
1. Some OEM vista cdkeys are interchanageable for 32 bit and 64 bit versions. I have tried my ultimate 32 bit vista key and it works gracefully with the 64 bit DVD.
2. Cheap stuff = bad compatibility. The wireless dongle i bought for 15 bucks now shows the weakness over a pci wireless card: no driver for vista 64. I have to hook up two 3 meter cable to reach the router, and i still have the plastic connector back 3 years ago. And it rocks!
3. Weird file protection issues. Ok, here's what it is. Some softwares like acrobat reader will create some protection over certain files even admin can't delete in the first few tries. You need to 'takeover' the file ownership then 'grant' it to new administrators. Luckily these commands supports *.* batches...otherwise i have to manually deal with hundreds of files.
If you got access denied:
takeown /f file_name
icacls file_name /grant administrators:F
Then you may delete all the files.
There may be a hidden manual that can turn the entire vista into commandline?
4. There was a weird *.mov file on my computer in vista 32 that i could not remove before. First i thought it was related to hardware failure (NOOOO!) Chkdsk was totally green. I can play this file, it was fine, but any other operations, like rename, cut, delete, even right click on properties will freeze the explorer. I turned off OAS still no luck. Some googling showed that ppl have encountered similar issues, but no clear solutions were provided. Besides, this was not related to privileges.
Now i will see how vista works with my 8G of ram.
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