User: laural710

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laural7100
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Posts by laural710

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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 5 months ago by laural7100
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Comment: C: msmsTests, NA values in test.results output
... DEP (load msmsTests & msmsEDA) pData(BaP_exp)$Group=rep(c("Ctrl","5"),each=3) > pData(BaP_exp)              sampleNames Group CTRL.a 20171124VS37.mzML  Ctrl CTRL.b 20171124VS38.mzML  Ctrl CTRL.c 20171124VS39.mzML  Ctrl BaP.5a 20171124VS40.mzML     5 BaP.5b 20171124VS41.mzML     5 BaP.5c 2017 ...
written 5 months ago by laural7100
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Comment: C: msmsTests, NA values in test.results output
... Many thanks for your quick reply. I've ran the code again and am now getting a new error message. I've updated my packages since i first asked my question, but i don't think that is what is going wrong. Library(MSGFplus, MSnbase, MSnID,vsn, imputeLCMD) > t1=c("20171124VS37.mzML") > q1=c("201 ...
written 5 months ago by laural7100
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Comment: C: msmsTests, NA values in test.results output
... How can i provide the code as its produced in R? Do i just copy it under the line of run code?  I've never been able to attach code before on this forum and am slightly lost. Sorry for the inconvenience ...
written 5 months ago by laural7100
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Comment: C: msmsTests, NA values in test.results output
... Many thanks for your quick reply. I've attached the code that i have used but i'm unsure if it is in the correct format? Any help would be greatly appreicated ...
written 5 months ago by laural7100
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Comment: C: msmsTests, NA values in test.results output
... BaP_Exp consists of 12 samples, 3 biological replicates of 4 conditions. The data below as been subsetted to two comparisons. BaP_exp is a large MSnSet. Code for analysis mix1=BaP_exp[,BaP_exp$Group %in% c("Ctrl","5")] new=pp.msms.data(mix1) pData(new) ##6 samples H0="y~" H1="y~Group" ...
written 5 months ago by laural7100 • updated 5 months ago by Laurent Gatto1.1k
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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 5 months ago by laural7100
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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 5 months ago by laural7100 • updated 5 months ago by Laurent Gatto1.1k
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Writing a loop to clean up protein names
... Hi All I'm not sure if this is even the correct forum to ask this. I wonder if anyone can offer some advice about where i am going wrong with a loop i'm trying to write for cleaning up UNIPROT data names.  Basically, the name i have from proteomics analysis is something like tr|A0A02DLI66|A0A02DLI ...
proteomics R transcriptomics loops batch-processing written 5 months ago by laural7100 • updated 5 months ago by Sebastian Gibb80
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Comment: C: Ortholog conversions of non-model organisms not present in Biomart, ensembl or K
... Thanks for that, and for now knowing someone else has had the same issues with this species as me even though its ironically a model species! It was an option but i managed to get to the point of GO enrichment using clusterProfiler and building a rainbow trout annotation package via AnnotationForge ...
written 6 months ago by laural7100

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