User: jspmccain

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jspmccain10
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Posts by jspmccain

<prev • 9 results • page 1 of 1 • next >
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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 12 months ago by jspmccain10
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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 12 months ago by jspmccain10 • updated 12 months ago by Aaron Lun25k
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Comment: C: Label free quantification post FDR calculation for MS/MS Proteomics
... Thanks for the detailed answer! ...
written 19 months ago by jspmccain10
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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 19 months ago by jspmccain10 • updated 19 months ago by Laurent Gatto1.2k
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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 21 months ago by jspmccain10
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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 21 months ago by jspmccain10
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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 21 months ago by jspmccain10 • updated 21 months ago by Ryan C. Thompson7.4k
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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 2.2 years ago by jspmccain10 • updated 2.2 years ago by Laurent Gatto1.2k
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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 2.3 years ago by jspmccain10 • updated 2.3 years ago by Michael Love26k

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