User: Michele Busby

gravatar for Michele Busby
Michele Busby1.8k
Reputation:
1,750
Status:
Trusted
Location:
United States
Website:
http://scotty.genetics...
Twitter:
michelebusby
Last seen:
9 hours ago
Joined:
5 years, 3 months ago
Email:
b************@gmail.com

Computational biologist at an oncology startup, formerly at the Broad Institute. I developed Scotty application for performing RNA Seq power analysis while completing my PhD in Gabor Marth's lab.

Posts by Michele Busby

<prev • 121 results • page 1 of 13 • next >
2
votes
2
answers
80
views
2
answers
Answer: A: quantification RNAseq and normalization
... Hi KML, I think you need to step back for a moment and think about what each measurement is good for. In general, you want to use counts when you are looking at the expression of one gene in multiple conditions and TPM when you are comparing or ranking the expression of different genes. You start ...
written 9 hours ago by Michele Busby1.8k
0
votes
2
answers
181
views
2
answers
Answer: A: How to remove the RIN (RNA integrity number) effect for RNA-seq data?
... You may want to try looking at the supplements for the GTEx papers. They did a lot of work on that. It also depends a lot on the protocol. If it is PolyA selected you will get biases against short genes because you will lose the 5' end. If it is RNA depleted or hybrid capture your bias will be diffe ...
written 20 days ago by Michele Busby1.8k
2
votes
1
answer
176
views
1
answers
Answer: A: Can I add TPM values of Isoforms of the same gene to get total gene expression?
... If they are calculated correctly (e.g. with RSEM or similar), the quantification should be divided among the isoforms in a mutually exclusive way. So if you have Isoform1 3 TPM - three transcripts Isoform2 1 TPM - one transcript The total gene should have 4 transcripts per million (i.e. 4 inde ...
written 3 months ago by Michele Busby1.8k
2
votes
2
answers
189
views
2
answers
Answer: A: Sub-typing patients by a single gene's expression in TCGA dataset.
... Do I understand correctly that you are dividing the samples by the expression of the gene (rather than observing the expression of the gene in different groups)? If so, the first thing I would do is make a histogram of the log TPM and see if it is bimodal. Then if it is you will know where the cuto ...
written 3 months ago by Michele Busby1.8k
0
votes
3
answers
3.6k
views
3
answers
Comment: C: ChIP seq- input DNA control for normalization
... Are sample A, B, and C the same biological sample? ...
written 5 months ago by Michele Busby1.8k
0
votes
3
answers
3.6k
views
3
answers
Comment: C: ChIP seq- input DNA control for normalization
... Yes, the PCR duplicates will be there but if you use paired end reads you can mark them and eliminate them from your analysis. ...
written 5 months ago by Michele Busby1.8k
2
votes
0
answers
348
views
0
answers
Job: Bioinformatics Scientist at Gritstone Oncology (Cambridge, MA)
... Hi All, We are looking for Bioinformatics Scientist to work on personalized oncology treatments at Gristone Oncology. Having started in NGS bioinformatics at the very beginning, it is amazing for me to see bioinformatics driving treatments that are put into patients. I really enjoy this work, and I ...
next-gen job rna-seq sequencing written 5 months ago by Michele Busby1.8k
1
vote
1
answer
347
views
1
answers
Answer: A: RSEM RNAseq - comparison between samples
... If it's RSEM from the archive version of TCGA then there is a field in there which is similar to TPM. See this entry: https://www.biostars.org/p/106127/ If someone ran RSEM more recently and you got that data from them then there is probably something like TPM in there somewhere. Since TPM is no ...
written 7 months ago by Michele Busby1.8k
0
votes
1
answer
337
views
1
answers
Answer: A: Are a Large Number of Biological Replicates Ever an Acceptable Replacement for T
... Yes. Biological replicates will contain both biological variance and technical variance. Therefore, when you run biological replicates you are often "blocking" on both biological noise and technical noise. Since these are usually uncorrelated, the total variance in the system is additive. Where t ...
written 7 months ago by Michele Busby1.8k
2
votes
3
answers
553
views
3
answers
Answer: A: Differential expression for two very different samples
... Since the main problem here would be drawing a line through the middle of the genes to normalize the two sets, if you are creating your own data you may want to spike in ERCCs. These are RNA sequences that you would put into each sample in the same quantity to assist with normalization later. In tr ...
written 10 months ago by Michele Busby1.8k

Latest awards to Michele Busby

Scholar 3 months ago, created an answer that has been accepted. For A: Coverage for sample with many species
Scholar 3 months ago, created an answer that has been accepted. For A: Coverage for sample with many species
Popular Question 8 months ago, created a question with more than 1,000 views. For Tool For Visualizing Sections Of Sequences
Commentator 13 months ago, created a comment with at least 3 up-votes. For C: Need Help For The Study Design Of A Rna-Seq Project
Appreciated 14 months ago, created a post with more than 5 votes. For A: How Do I Get Started Working With Rna-Seq Data
Teacher 15 months ago, created an answer with at least 3 up-votes. For A: Coverage for sample with many species
Scholar 16 months ago, created an answer that has been accepted. For A: Coverage for sample with many species
Teacher 16 months ago, created an answer with at least 3 up-votes. For A: Coverage for sample with many species
Centurion 16 months ago, created 100 posts.
Scholar 17 months ago, created an answer that has been accepted. For A: Coverage for sample with many species
Appreciated 23 months ago, created a post with more than 5 votes. For A: What Is The Best Tool For Power Analysis For An Rna-Seq Experimental Design
Teacher 24 months ago, created an answer with at least 3 up-votes. For A: Coverage for sample with many species
Teacher 2.2 years ago, created an answer with at least 3 up-votes. For A: Coverage for sample with many species
Commentator 2.4 years ago, created a comment with at least 3 up-votes. For C: Need Help For The Study Design Of A Rna-Seq Project
Teacher 3.0 years ago, created an answer with at least 3 up-votes. For A: Coverage for sample with many species
Guru 3.1 years ago, received more than 100 upvotes.
Teacher 3.2 years ago, created an answer with at least 3 up-votes. For A: Coverage for sample with many species
Commentator 3.5 years ago, created a comment with at least 3 up-votes. For C: Need Help For The Study Design Of A Rna-Seq Project
Teacher 3.6 years ago, created an answer with at least 3 up-votes. For A: Coverage for sample with many species
Good Answer 3.7 years ago, created an answer that was upvoted at least 5 times. For A: What Is The Best Tool For Power Analysis For An Rna-Seq Experimental Design
Scholar 3.9 years ago, created an answer that has been accepted. For A: Coverage for sample with many species
Teacher 3.9 years ago, created an answer with at least 3 up-votes. For A: What Is The Best Tool For Power Analysis For An Rna-Seq Experimental Design

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1588 users visited in the last hour