User: Steve Shen

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Steve Shen330
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Posts by Steve Shen

<prev • 33 results • page 1 of 4 • next >
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FYI: Junior bioinformatian positions available
... Dear friends, Our institute is seeking bioinformatians, master level with 0-2 years experiences and opportunity to join biomedical informatics Ph.D program. If someone or someone you know is interested, please let me know. I will send the job description over, because I don't think it's proper to p ...
written 5.6 years ago by Steve Shen330
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Comment: C: LIMMA with beta distributed data
... Hi Sunny, Thanks so much. I am not using LIMMA for microarray data in this case. I like LIMMA because of its capability of modeling and ebays function. It will be a big plus if LIMMA can deal with other type of data. Thanks again and much appreciated. Speaking zero in this case, it is the true obs ...
written 8.3 years ago by Steve Shen330
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Comment: C: LIMMA with beta distributed data
... Hi Sunny, Thanks so much for your input. Then, how to deal with inf or missing value after logit, because the data I am dealing with have lots of zeros in many samples. Any opinion? I wish that LIMMA can provide some link/family type of arguments just like GLM does. Thanks a lot. Steve On Wed, Ma ...
written 8.3 years ago by Steve Shen330
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LIMMA with beta distributed data
... Hello list, Can LIMMA work with beta distributed interval(0,1) data? Thanks, Steve [[alternative HTML version deleted]] ...
limma written 8.3 years ago by Steve Shen330 • updated 8.3 years ago by Sunny Srivastava340
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basic stats for methylC-seq type of methylation data
... Dear All, I really appreciate if someone could help me out with this basic statistical problem or provide some suggestions. I have a set of bisulphite methylation data (methylC-seq) at single base resolution. The mapping information for each base is including coverage (2-20X) and frequency of methy ...
coverage written 8.4 years ago by Steve Shen330
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Comment: C: forge BSgenome data package
... Hi Herve, Thanks so much for your time and advices. Best, Steve 2011/1/28 Hervé Pagès > Hi Steve, > > > On 01/27/2011 10:37 PM, Steve Shen wrote: > >> Hi Herve, >> >> Sorry for bothering you again. With you help, I was able to build this >> BSgenome data p ...
written 8.5 years ago by Steve Shen330
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Comment: C: forge BSgenome data package
... Hi Herve, Sorry for bothering you again. With you help, I was able to build this BSgenome data package. Now it brings me another level of problem. How do I manipulate the sequences since it is quite different from the examples in your documentation? For example, how can I find the sequences that le ...
written 8.5 years ago by Steve Shen330
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Comment: C: forge BSgenome data package
... Hi Herve, Thank you very very much for your time and very valuable advice. The distributable standard data package is definitely a way to go. Since the genomes I am working on are still in evolvement, there are lots of problems with current version of contigs and scaffolds. However, I will try it a ...
written 8.5 years ago by Steve Shen330
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Comment: C: forge BSgenome data package
... Hi Herve, Sorry about that I forgot using reply all. Below is my seed file. I am dealing with a brand new genome that was published a couple of months ago. The genome consists of lots of scaffolds and contigs, no chromosome information available. That's why it looks weird. Yous explanation and sugg ...
written 8.5 years ago by Steve Shen330
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Comment: C: forge BSgenome data package
... Hi Herve, Thank you very much. I tried carefully with correct path and file name by triggering auto-complete feature. But it didn't help either. It may be something wrong with my seed file, so I also appended the file below. Please have a look. Thanks in advance, Steve > forgeBSgenomeDataPkg(" ...
written 8.5 years ago by Steve Shen330

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