User: fgol
fgol • 10
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Posts by fgol
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... Hello. I am doing ensemble gene set testing using EGSEA (Ensemble of Gene Set Enrichment Analyses) from the edgeR output. I have a list of Ensembl gene IDs from edgeR (dge variable), that I found that after voom transformation, I need to build an index for each gene set collection using the EGSEA in ...
written 6 weeks ago by
fgol • 10
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... Thanks a lot for your useful help. ...
written 7 months ago by
fgol • 10
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... Thank you very much. It is very good that I can do quantification from this identification dataset, while I do not have raw data.
May I also know for quantification through spectral counting using MSnbase, which of the features (from my above list) will be used to do spectral counting and quantific ...
written 7 months ago by
fgol • 10
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... Thanks for your reply. This dataset is only an identification dataset, and I asked the person in charge of running MS about protein quantitation values. He said this experiment is not designed for protein quantitation. I do not know why. Maybe because it is an immuno-precipitation experiment.
The on ...
written 7 months ago by
fgol • 10
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... Hello,
I received a dataset (from proteome discoverer) containing the below information for both protein and peptide levels:
Protein level:
Accession
Description
Exp. q-value
Sum PEP Score
Coverage
Peptides
PSMs
Unique Peptides
AAs
MW [kDa]
calc. pI
Score Sequest HT
Peptides Sequest HT
...
written 7 months ago by
fgol • 10
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... Many thanks for your great help. It is working now and I could also add my phenoData.csv to the final MSnSet file. Thanks a lot. ...
written 8 months ago by
fgol • 10
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... Hello gain,
I need to learn how I can create an MSnSet file from a csv file. So, as an example, I just wrote “msms.spk” expression dataset (from “msmsTests” package) to a csv file as bellow:
library(msmsTests)
data(msms.spk)
write.exprs(msms.spk, file="msms.txt", sep="\t")
Then, I man ...
written 8 months ago by
fgol • 10
• updated
8 months ago by
Laurent Gatto ♦ 1.2k
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... That was great. I could create both files (csv and MSnSet files). Thanks a lot Laurent. ...
written 8 months ago by
fgol • 10
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... Hello,
I have a “xlsx” quantitative dataset from proteome discoverer software (the xlsx matrix file contains rows as identified proteins and columns as different conditions/treatments, and matrix cells corresponds to spectral counts).
I need to convert my xlsx dataset to MSnSet format to be able t ...
written 8 months ago by
fgol • 10
• updated
8 months ago by
Laurent Gatto ♦ 1.2k
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... Dear Laurent,
Thank you very much. You are right, it shows file number 6 is README file. However, still I have the same problem when I try to open file number 7, and also 8.
> px1 <- PXDataset("PXD000001")
> mzf <- pxget(px1, 7)
Downloading 1 file
trying URL 'ftp://ftp.p ...
written 8 months ago by
fgol • 10
• updated
8 months ago by
Laurent Gatto ♦ 1.2k
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