User: jspmccain

gravatar for jspmccain
jspmccain10
Reputation:
10
Status:
New User
Location:
Last seen:
6 months, 1 week ago
Joined:
1 year, 10 months ago
Email:
j********@gmail.com

Posts by jspmccain

<prev • 9 results • page 1 of 1 • next >
0
votes
1
answer
184
views
1
answers
Comment: C: edgeR DE analysis: single group combined factors or GLM with interaction term
... That's great, thanks for such an in-depth answer! I hadn't thought about how dispersion estimates would change when removing significant interactions. ...
written 6 months ago by jspmccain10
2
votes
1
answer
184
views
1
answer
edgeR DE analysis: single group combined factors or GLM with interaction term
... I've been reading about the difference between using a GLM in one of two ways: 1) y ~ 0 + all-group-combinations or 2) y ~ 1 + group1 + group2 + group1:group2. I know that in the edgeR user's guide it recommends the first approach (section 3.2.4). I understand that this approach is advantageous bec ...
edger glm written 6 months ago by jspmccain10 • updated 6 months ago by Aaron Lun24k
0
votes
1
answer
255
views
1
answers
Comment: C: Label free quantification post FDR calculation for MS/MS Proteomics
... Thanks for the detailed answer! ...
written 13 months ago by jspmccain10
1
vote
1
answer
255
views
1
answer
Label free quantification post FDR calculation for MS/MS Proteomics
... I'm using MS/MS for label-free quantification in metaproteomics. I've run the database searching (MSGF+) with mzML files, and the output is .mzid files. Then, I've used the MSnID and mzid R packages to calculate/optimize False Discovery Rate cutoffs, and applied these cutoffs. I'm confused about whe ...
mzr mzid msnbase written 13 months ago by jspmccain10 • updated 13 months ago by Laurent Gatto1.1k
0
votes
1
answer
336
views
1
answers
Comment: C: Fitting Gamma GLMs for examining differential expression
... This link is an extremely helpful description of the TMT normalization method, and the other related links go into the statistical consequences of it! https://github.com/pwilmart/IRS_normalization/blob/master/.ipynb_checkpoints/understanding_IRS-checkpoint.ipynb ...
written 15 months ago by jspmccain10
0
votes
1
answer
336
views
1
answers
Comment: C: Fitting Gamma GLMs for examining differential expression
... This is super helpful, thank you for the limma suggestion, and for your filtering criterion insight. I will be looking into the application of limma, and to be honest I'm still trying to understand the empirical Bayes estimation of biological variability.  Regarding the filtering criterion my under ...
written 15 months ago by jspmccain10
6
votes
1
answer
336
views
1
answer
Fitting Gamma GLMs for examining differential expression
... It's my understanding that negative binomial GLMs are used in different ways in both EdgeR and DeSeq2. Both of these packages assume the input are un-normalized counts. I am working with proteomics data from a mass spectrometer. Specifically, I'm using TMT-Labeling to quantify changes in differentia ...
edger deseq2 differential expression written 15 months ago by jspmccain10 • updated 15 months ago by Ryan C. Thompson7.3k
3
votes
2
answers
352
views
2
answers
Extract whether list element is MS1 or MS2 from mzR::peaks() output
... I'm working the R package mzR for extracting raw data from a mzMXL file. I'd like to examine the distribution of ion intensities from MS1 only, is there a way to differentiate the MS1 scans from MS2 scans via the *peaks()* function? Right now I'm just filtering the elements of the list by the range ...
mzr written 20 months ago by jspmccain10 • updated 20 months ago by Laurent Gatto1.1k
1
vote
1
answer
531
views
1
answer
Using Normalized Values in DeSeq2 - Metatranscriptomics
... I am analyzing a time series of a metatranscriptome. In metatranscriptomics, we have to do the regular normalizations found in RNA-Seq (ie. gene sequence length, and sample-differences in total expression). However, there is an additional normalization required to account for changes in species abun ...
deseq2 written 22 months ago by jspmccain10 • updated 22 months ago by Michael Love24k

Latest awards to jspmccain

No awards yet. Soon to come :-)

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 16.09
Traffic: 284 users visited in the last hour