User: yockpingchow

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Posts by yockpingchow

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Comment: C: RforProteomics workflow troubleshooting
... script: part 2 library("rTANDEM") param <- setParamOrbitrap() taxonomy <- rTTaxo(taxon="hsapiens",                    format="peptide",                    URL= "h_sapines_fwd_rev.fasta") param <- setParamValue(param, 'list path', 'taxonomy information', taxonomy) param <- setParamValue( ...
written 17 months ago by yockpingchow0
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Comment: C: RforProteomics workflow troubleshooting
... The script as shown below: library("rpx") id <- "PXD002081" px <- PXDataset(id) try(setInternet2(FALSE),silent=TRUE) library("jsonlite") addr <- "http://www.ebi.ac.uk:80/pride/ws/archive/%s/list/project/%s" files <- fromJSON(sprintf(addr, "file", id))$list assays <- fromJSON(sprintf ...
written 17 months ago by yockpingchow0
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Comment: C: RforProteomics workflow troubleshooting
... Hi, Thanks very much for the guidance. I managed to run through the demo data. Now, I have problem with real public data (PXD002081). I have no idea why  R been forced to shut down when performing this step:   The error message : <br>Fatal error:non-standard CO ...
written 17 months ago by yockpingchow0
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Comment: C: RforProteomics workflow troubleshooting
... Hi, I have run following scripts, still the same. > if (!allfiles) { +     library("R.utils") +     sapply(list.files(pattern = "mzML.gz"), gunzip) + } > output.files <- lapply(sub("\\.gz","",files$fileName), + function(x){ + param <- setParamValue(param,  'spectrum' ,  'path' , valu ...
written 17 months ago by yockpingchow0
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Comment: C: RforProteomics workflow troubleshooting
... Hi,  I am still having the same problem: > files$fileName  [1] "c_elegans_C_1_3_21Apr10_Draco_10-03-06.mzML.gz" "c_elegans_E_3_1_21Apr10_Draco_10-03-04.mzML.gz"  [3] "c_elegans_E_3_3_21Apr10_Draco_10-03-04.mzML.gz" "c_elegans_D_1_3_21Apr10_Draco_10-03-07.mzML.gz"  [5] "c_elegans_D_1_1_21Apr10_Dr ...
written 17 months ago by yockpingchow0
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RforProteomics workflow troubleshooting
... Hi, I have problem with RforProteomics workflow and wish to get help to solve it. I am running through the part 6 "A comprehensive example" in manual "Using R for proteomics data analysis", and got this error  when performed the step in "peptide identification": The errors: > output.files < ...
proteomics written 17 months ago by yockpingchow0

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