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Search: Posts Made By: Nepa10
Forum: Bioinformatics 09-23-2014, 08:12 PM
Replies: 3
Views: 7,128
Posted By Nepa10
Hi, thank you very much. I realized that...

Hi, thank you very much. I realized that Psi-blast is an option available through blastp. Seems like Psi-blast is more rigorous that blastX.

I am little bit confused about the difference between...
Forum: Bioinformatics 09-21-2014, 06:05 PM
Replies: 3
Views: 7,128
Posted By Nepa10
tblastn and blastx question

It says that tblastn is more likely to find distantly related sequences than the blast, blasts, and blastp. I wonder why is it? I generally use Blastx.

By definition, tblastn compares query...
Forum: Bioinformatics 07-27-2014, 05:24 PM
Replies: 0
Views: 1,393
Posted By Nepa10
GC-content normalization

Can anyone please explain the how the normalization is done for GC-content bias?

I read the papers but could not get the grasp of the statistical method used.

"Understanding mechanisms...
Forum: Bioinformatics 07-25-2014, 08:34 PM
Replies: 7
Views: 4,884
Posted By Nepa10
Thank you very much. Appreciate it!

Thank you very much. Appreciate it!
Forum: Bioinformatics 07-17-2014, 07:48 AM
Replies: 7
Views: 4,884
Posted By Nepa10
Yes I got the function you use to calculate TMM...

Yes I got the function you use to calculate TMM from that paper. It uses R function, calcNormFactors().

However I was wondering if I could manually calculate it using the formula I mentioned...
Forum: Bioinformatics 07-16-2014, 05:44 AM
Replies: 7
Views: 4,884
Posted By Nepa10
Thank you for the quick response and...

Thank you for the quick response and clarification. Would you mind providing some insight into how the calculation is done and what that component factor stands for in the equation.


Thanks!
Forum: Bioinformatics 07-15-2014, 02:06 PM
Replies: 7
Views: 4,884
Posted By Nepa10
calculate TMM normalization

Hello all,

I would like to calculate TMM normalization for identifying DE genes. I know that edgeR does all the normalization when you run the code but I would like to calculate TMM for one or...
Forum: Bioinformatics 06-05-2014, 08:57 PM
Replies: 0
Views: 1,231
Posted By Nepa10
Post validation of Differentially expressed data with real-time PCR

Hello all:

I am trying to validate my DE genes acquired from running RSEM. I am confused as to how many genes and how many samples should be tested. I would really appreciate if you guys could...
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