User: fgol

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fgol10
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Posts by fgol

<prev • 14 results • page 1 of 2 • next >
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How an index is built for each gene set collections using buildCustomIdx() indexing function of EGSEA package?
... 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 ...
limma biomart edger rna-seq egsea written 6 weeks ago by fgol10
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Comment: C: Protein quantification by MSnbase package
... Thanks a lot for your useful help. ...
written 7 months ago by fgol10
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Comment: C: Protein quantification by MSnbase package
... 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 fgol10
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Answer: A: Protein quantification by MSnbase package
... 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 fgol10
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Protein quantification by MSnbase package
... 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 ...
msnbase rforproteomics written 7 months ago by fgol10
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Comment: C: How to convert a xlsx data file to MSnSet format?
... 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 fgol10
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Answer: A: How to convert a xlsx data file to MSnSet format?
... 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 fgol10 • updated 8 months ago by Laurent Gatto1.2k
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Comment: C: How to convert a xlsx data file to MSnSet format?
... That was great. I could create both files (csv and MSnSet files). Thanks a lot Laurent. ...
written 8 months ago by fgol10
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How to convert a xlsx data file to MSnSet format?
... 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 ...
proteomics msnbase msnid msmstests lc-ms/ms written 8 months ago by fgol10 • updated 8 months ago by Laurent Gatto1.2k
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Comment: C: MSnbase package, Error in downloading data file "PXD000001" from PRIDE Repositor
... 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 fgol10 • updated 8 months ago by Laurent Gatto1.2k

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