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Messages - prasadpb

1
XCMS / Re: memory error during fillpeak step
Quote from: "Ralf"
Quote
I there any way out?

Yes there is. Simply purchase sufficient RAM for your workstation.
I mean can I generate just peak report (without 'mullest' comparison) for those two chromatograms without doing fillPeaks()?
Thanks
2
XCMS / Re: memory error during fillpeak step
Dear XCMS users,
I am facing same problem with my just two data files of 30 min run from Q-exactive after converting them to cdf file (each file goes upto 1.3 GB )
Initially working with my data of 30 samples. I faced problem of memory allocation over 40000MB, So I decided to run with just two samples. They work fine until peakFill() and got following error.
How I can process my data using 64bit PC with 4GB RAM, as with just 2 samples only I am getting memory error.
I there any way out?

Please help.



> xset2<-fillPeaks(xset1)
NS-Coat-161212-STG-1 Error: cannot allocate vector of size 840.9 Mb
In addition: Warning messages:
1: In mzR:::netCDFRawData(cdf) :
  Reached total allocation of 4004Mb: see help(memory.size)
2: In mzR:::netCDFRawData(cdf) :
  Reached total allocation of 4004Mb: see help(memory.size)
3: In mzR:::netCDFRawData(cdf) :
  Reached total allocation of 4004Mb: see help(memory.size)
4: In mzR:::netCDFRawData(cdf) :
  Reached total allocation of 4004Mb: see help(memory.size)







R Under development (unstable) (2012-12-01 r61188)
Platform: x86_64-w64-mingw32/x64 (64-bit)

locale:
[1] LC_COLLATE=English_United States.1252  LC_CTYPE=English_United States.1252    LC_MONETARY=English_United States.1252 LC_NUMERIC=C                         
[5] LC_TIME=English_United States.1252   

attached base packages:
[1] parallel  stats    graphics  grDevices utils    datasets  methods  base   

other attached packages:
[1] multtest_2.14.0    Biobase_2.19.1    BiocGenerics_0.5.1 xcms_1.34.0        mzR_1.5.2          Rcpp_0.10.1     

loaded via a namespace (and not attached):
[1] codetools_0.2-8  MASS_7.3-22      splines_2.16.0  stats4_2.16.0    survival_2.36-14
>
3
XCMS / Re: mzR Error for XCMS
I used new binary packages of mzR, version 1.5.4 (devel) and worked fine with 32 bit system. But my R is getting crashed.
So, I switched to 64 bit PC and it works. But my 32 bit system still get crashed for R with this.
Anyway thanks I am working with 64 bit system and its fine.
Thanks a lot.
5
XCMS / Re: mzR Error for XCMS
Dear,
I switched to 64 bit PC with same versions of Bioc and R.
Surprisingly mzR error gone and it works fine now.
But still couldn't understand whats wrong with 32bit PC, still trying to solve and any clues?

Prasad...
7
XCMS / Re: mzR Error for XCMS
R Under development (unstable) (2012-12-01 r61188)
Platform: i386-w64-mingw32/i386 (32-bit)

locale:
[1] LC_COLLATE=English_United States.1252  LC_CTYPE=English_United States.1252    LC_MONETARY=English_United States.1252
[4] LC_NUMERIC=C                          LC_TIME=English_United States.1252   

attached base packages:
[1] parallel  stats    graphics  grDevices utils    datasets  methods  base   

other attached packages:
[1] Biobase_2.19.1    BiocGenerics_0.5.1 Rcpp_0.10.1     

loaded via a namespace (and not attached):
[1] tools_2.16.0
8
XCMS / Re: mzR Error for XCMS
Hi,
I tried your 3 suggetions but still getting error which is different from previous.
Here is my script for your review.

Thanks.


> library(methods)
> library(BiocGenerics)

Attaching package: ‘BiocGenerics’

The following object is masked from ‘package:stats’:

    xtabs

The following objects are masked from ‘package:base’:

    anyDuplicated, cbind, colnames, duplicated, eval, Filter, Find, get, intersect, lapply, Map, mapply, mget,
    order, paste, pmax, pmax.int, pmin, pmin.int, Position, rbind, Reduce, rep.int, rownames, sapply, setdiff,
    table, tapply, union, unique

> library(BiocGenerics)
> library(Biobase)
Welcome to Bioconductor

    Vignettes contain introductory material; view with 'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.

> library(Biobase)
> library(Rcpp)
> library(mzR)
Error : .onLoad failed in loadNamespace() for 'mzR', details:
  call: value[[3L]](cond)
  error: failed to load module Ramp from package mzR
negative length vectors are not allowed
Error: package or namespace load failed for ‘mzR’
>
9
XCMS / Re: mzR Error for XCMS
Thanks,
I dowloaded and installed package BiocGenerics_0.4.0.zip and tried on R-2.16 (devel),
but with same error.
> utils:::menuInstallLocal()
package ‘BiocGenerics’ successfully unpacked and MD5 sums checked
> library(mzR)
Error : objects ‘annotation’, ‘annotation<-’ are not exported by 'namespace:BiocGenerics'
Error: package or namespace load failed for ‘mzR’

Please guide further.

Prasad..
10
XCMS / Re: mzR Error for XCMS
Thanks for reply,

Packages I a using are
BioCGenerics_0.2.0
Biobase_2.19.1
Rcpp_0.10.1
mzR_1.4.1

Is this combination is fine or need more updates?
I tried several times changing R 2.15.0, 2.15.2 and 2.16.0
Getting same error-
> library(mzR)
Loading required package: Rcpp
Error : objects ‘annotation’, ‘annotation<-’ are not exported by 'namespace:BiocGenerics'
Error: package/namespace load failed for ‘mzR’


Please help me out.

Prasad
11
XCMS / mzR Error for XCMS
Dear all,
Please help for this.
Although I have installed and unpacked mzR folder for R 2.15.2 version. I am getting this error continuously.
Loading required package: mzR
Error : objects ‘annotation’, ‘annotation<-’ are not exported by 'namespace:BiocGenerics'
Error: package ‘mzR’ could not be loaded

ALSO, HOW CAN I GET CORRECT SET OF XCMS AND RELATED PACKAGES FOR R 2.15.2.
12
XCMS Online / UPLC-SQD parameters
Dear,
I am using data from Waters UPLC-SQD system.
Kindly, upgrade the parameters for the same.
Or please suggest me alternative to process such data.
Thank you...

Warm Regards,

Prasad