I am doing a tutorial about Quantitative Proteomics using rpx to import data an PXDataset keep giving me error in fpt connexion.
Is there any way to load all needed data into "px1" without the need to download it from fpt? I downloaded all needed files in local. I both tried from behind a firewall and not.
Yes, indeed, if you have local files, you can provide their full path as input to the openMSfile() function. This is also what happens in the example above, except that the path to the local file is extracted from the rpx cache once it has been downloaded.
I would highly advise to have a look at the more recent Bioconductor packages and teaching material, all described in the R for Mass Spectrometry handbook.
It looks like there was a problem to access and download files from the PRIDE ftp server. Things seem to work on my end now:
> library(rpx)
> px1 <- PXDataset("PXD000001")
> px1
Object of class "PXDataset"
Id: PXD000001 with 12 files
[1] 'F063721.dat' ... [12] 'generated'
Use 'pxfiles(.)' to see all files.
> pxfiles(px1)
[1] "F063721.dat"
[2] "F063721.dat-mztab.txt"
[3] "PRIDE_Exp_Complete_Ac_22134.xml.gz"
[4] "PRIDE_Exp_mzData_Ac_22134.xml.gz"
[5] "PXD000001_mztab.txt"
[6] "README.txt"
[7] "TMT_Erwinia_1uLSike_Top10HCD_isol2_45stepped_60min_01-20141210.mzML"
[8] "TMT_Erwinia_1uLSike_Top10HCD_isol2_45stepped_60min_01-20141210.mzXML"
[9] "TMT_Erwinia_1uLSike_Top10HCD_isol2_45stepped_60min_01.mzXML"
[10] "TMT_Erwinia_1uLSike_Top10HCD_isol2_45stepped_60min_01.raw"
[11] "erwinia_carotovora.fasta"
[12] "generated"
> mzf <- pxget(px1, 6)
Downloading 1 file
trying URL 'ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2012/03/PXD000001/README.txt'
Content type 'unknown' length 1645 bytes
==================================================
> mzf
[1] "/home/lg390/tmp/README.txt"
There is however another point you need to be careful with. File number 6 isn't a raw file, but the README file. You need to first check file indices to identify those that you want to downloaded. In this case, it seems to be file number 7.
> mzf <- pxget(px1, 7)
Downloading 1 file
trying URL 'ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2012/03/PXD000001/TMT_Erwinia_1uLSike_Top10HCD_isol2_45stepped_60min_01-20141210.mzML'
Content type 'unknown' length 450032788 bytes (429.2 MB)
==================================================
> mzf
[1] "/home/lg390/tmp/TMT_Erwinia_1uLSike_Top10HCD_isol2_45stepped_60min_01-20141210.mzML"
> openMSfile(mzf)
Mass Spectrometry file handle.
Filename: TMT_Erwinia_1uLSike_Top10HCD_isol2_45stepped_60min_01-20141210.mzML
Number of scans: 7534
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.
Hello, I have the same exact problem.
I am doing a tutorial about Quantitative Proteomics using rpx to import data an PXDataset keep giving me error in fpt connexion. Is there any way to load all needed data into "px1" without the need to download it from fpt? I downloaded all needed files in local. I both tried from behind a firewall and not.
Thank you very much for your help
gianluigi
Yes, indeed, if you have local files, you can provide their full path as input to the
openMSfile()function. This is also what happens in the example above, except that the path to the local file is extracted from the rpx cache once it has been downloaded.I would highly advise to have a look at the more recent Bioconductor packages and teaching material, all described in the R for Mass Spectrometry handbook.