User: queso012

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queso0120
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Posts by queso012

<prev • 8 results • page 1 of 1 • next >
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extract raw expression values in oligo package
... Hi,   How can we extract raw expression values in the oligo package?   I have Affymetrix, ST arrays and would like to obtain a matrix of raw expression values.   I tried the exprs function, however that gave me a million rows for the probes…I guess it wasn't summarized into probesets yet?. ra ...
oligo affymetrix raw expression written 3.3 years ago by queso0120
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Comment: C: msnbase error when adding identification data
... Thanks -- I was able to successfully connect, however I still receive an error at the addition of the identification step: > msexp <- addIdentificationData(rawdata, filenames = identFile, verbose = FALSE) Error in basename(id$spectrumFile) : a character vector argument expected > session ...
written 3.9 years ago by queso0120
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Comment: C: msnbase error when adding identification data
... Thanks for the solutions! I was able to successfully install boot2docker for mac, run bioconductor/devel_base R and install and load MSnbase. However, I cannot access my local drive ( I cannot set the working directory). Any suggestions on how to accomplish this?  ...
written 3.9 years ago by queso0120
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Comment: C: msnbase error when adding identification data
... Also, I have already taken a look at the thread posted here regarding the issue. It seems to not be resolved yet: https://github.com/lgatto/MSnbase/issues/39 ...
written 3.9 years ago by queso0120
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msnbase error when adding identification data
... Hi, I'm trying to msnbase to process my itraq data. I'm getting an error message when I try to add identification data. Please see my code and error message below. My raw data input is mzXML files  (.raw converted to mzXML using Proteowizard) and my mzIdent files are from Mascot. files=dir("/User ...
proteomics itraq msnbase written 3.9 years ago by queso0120 • updated 3.9 years ago by Laurent Gatto1.0k
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Comment: C: Isobar - generating IBSpectra object
...   Hi Thomas,   Thanks for your suggestions! So I was able to successfully parse my mzIdentML file using the mzID package. I was able to extract out the following fields: > names(flatResults)  [1] "spectrumid"                          "acquisitionnum"                      "calculatedmasstochar ...
written 3.9 years ago by queso0120
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Isobar - generating IBSpectra object
... Hi, I'm having trouble at the first step of reading in data and generating a IBSpectra object. I am using the readIBSpectra() function. From the documentation the id.file parameter can be mzIdentml or .csv. I have both formats which I exported from a mascot search. When I try both mzid or csv, I re ...
proteomics isobar itraq mzid mgf written 3.9 years ago by queso0120 • updated 3.9 years ago by Laurent Gatto1.0k
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isobar and iTRAQ data
... Dear All,     I have .raw files from iTRAQ and I'm a trying use the isobar bioconductor package. The input file formats for this package is csv and mgf formats. I was able to convert my .raw files to mgf format (using Proteowizard/msconverter) and .raw to mzXML format.  Does anyone have any sugge ...

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