User: laural710

gravatar for laural710
laural7100
Reputation:
0
Status:
New User
Last seen:
4 days, 16 hours ago
Joined:
1 year, 10 months ago
Email:
l********@msn.com

Profile information, website and location are not shown for new users.

This helps us discourage the inappropriate use of our site.

Posts by laural710

<prev • 20 results • page 1 of 2 • next >
0
votes
0
answers
38
views
0
answers
Comment: C: Writing a loop through multiple fasta files and named files (is it possible with
... That's what i was beginning to think. At the moment, the run is failing with a GC overhead limit error, and i have been trying to figure out if there is a work around, such as splitting the fasta files. Thanks for answering. ...
written 4 days ago by laural7100
0
votes
0
answers
38
views
0
answers
Writing a loop through multiple fasta files and named files (is it possible with MSGFplus?)
... When working with well annotated species, i can straight call MSGFplus and run this on the pure fasta file without any memory issues. However, due to poor protein annotation of a species i am working on, i need to use a large fasta file (>150,000 protein sequences). I have split this fasta up int ...
proteomics R msgf+ written 4 days ago by laural7100 • updated 4 days ago by Martin Morgan ♦♦ 23k
0
votes
1
answer
374
views
1
answers
Comment: C: msmsTests, NA values in test.results output
... Thanks. Turns out it was | operator that seemed to be throwing it off. Many thanks.  ...
written 12 months ago by laural7100
0
votes
1
answer
374
views
1
answers
Comment: C: msmsTests, NA values in test.results output
... DEP (load msmsTests & msmsEDA) pData(BaP_exp)$Group=rep(c("Ctrl","5"),each=3) > pData(BaP_exp)              sampleNames Group CTRL.a 20171124VS37.mzML  Ctrl CTRL.b 20171124VS38.mzML  Ctrl CTRL.c 20171124VS39.mzML  Ctrl BaP.5a 20171124VS40.mzML     5 BaP.5b 20171124VS41.mzML     5 BaP.5c 2017 ...
written 12 months ago by laural7100
0
votes
1
answer
374
views
1
answers
Comment: C: msmsTests, NA values in test.results output
... Many thanks for your quick reply. I've ran the code again and am now getting a new error message. I've updated my packages since i first asked my question, but i don't think that is what is going wrong. Library(MSGFplus, MSnbase, MSnID,vsn, imputeLCMD) > t1=c("20171124VS37.mzML") > q1=c("201 ...
written 12 months ago by laural7100
0
votes
1
answer
374
views
1
answers
Comment: C: msmsTests, NA values in test.results output
... How can i provide the code as its produced in R? Do i just copy it under the line of run code?  I've never been able to attach code before on this forum and am slightly lost. Sorry for the inconvenience ...
written 12 months ago by laural7100
0
votes
1
answer
374
views
1
answers
Comment: C: msmsTests, NA values in test.results output
... Many thanks for your quick reply. I've attached the code that i have used but i'm unsure if it is in the correct format? Any help would be greatly appreicated ...
written 12 months ago by laural7100
0
votes
1
answer
374
views
1
answers
Comment: C: msmsTests, NA values in test.results output
... BaP_Exp consists of 12 samples, 3 biological replicates of 4 conditions. The data below as been subsetted to two comparisons. BaP_exp is a large MSnSet. Code for analysis mix1=BaP_exp[,BaP_exp$Group %in% c("Ctrl","5")] new=pp.msms.data(mix1) pData(new) ##6 samples H0="y~" H1="y~Group" ...
written 12 months ago by laural7100 • updated 12 months ago by Laurent Gatto1.2k
0
votes
1
answer
374
views
1
answers
Comment: C: msmsTests, NA values in test.results output
... No, this is what is frustrating me. As part of the preparation of my experimental MSnSet, i remove any lines with NA (pNA=1/3 and then impute any remaining NA values with knn). When combining the data set, i use imputation QRILC to ensure that there are no NA values and then check with (is.na(exprs( ...
written 12 months ago by laural7100
2
votes
1
answer
374
views
1
answer
msmsTests, NA values in test.results output
... Hi All I'm strugglin with the analysis of DEP in a protein dataset i have. I have managed to analyse to this point in R using variants of MSGF etc and quantified via SI. Having run the samples via DAPAR and Prostar, i have knowldege of the number (or at least the region) of DEP to expect in this pa ...
proteomics fdr msmstests written 12 months ago by laural7100 • updated 12 months ago by Laurent Gatto1.2k

Latest awards to laural710

No awards yet. Soon to come :-)

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 16.09
Traffic: 406 users visited in the last hour