User: laural710

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laural7100
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Posts by laural710

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proteoQC throwing error after running
... The proteoQC package is exactly what i was looking for to give me some QC information on proteomic samples, however i am running into two issues. One may be a bug, and the other may be me doing something weird. The first is that when i am creating the sample list to run with the mQCpipe, it will on ...
proteomics proteoqc written 27 days ago by laural7100
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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 7 weeks ago by laural7100
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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 7 weeks ago by laural7100 • updated 7 weeks ago by Martin Morgan ♦♦ 24k
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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 13 months ago by laural7100
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Comment: C: msmsTests, NA values in test.results output
... DEP (load msmsTests & msmsEDA) pData(BaP_exp)$Group=rep(c("Ctrl","5"),each=3) > pData(BaP_exp)              sampleNames Group CTRL.a 20171124VS37.mzML  Ctrl CTRL.b 20171124VS38.mzML  Ctrl CTRL.c 20171124VS39.mzML  Ctrl BaP.5a 20171124VS40.mzML     5 BaP.5b 20171124VS41.mzML     5 BaP.5c 2017 ...
written 13 months ago by laural7100
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Comment: C: msmsTests, NA values in test.results output
... Many thanks for your quick reply. I've ran the code again and am now getting a new error message. I've updated my packages since i first asked my question, but i don't think that is what is going wrong. Library(MSGFplus, MSnbase, MSnID,vsn, imputeLCMD) > t1=c("20171124VS37.mzML") > q1=c("201 ...
written 13 months ago by laural7100
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Comment: C: msmsTests, NA values in test.results output
... How can i provide the code as its produced in R? Do i just copy it under the line of run code?  I've never been able to attach code before on this forum and am slightly lost. Sorry for the inconvenience ...
written 13 months ago by laural7100
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Comment: C: msmsTests, NA values in test.results output
... Many thanks for your quick reply. I've attached the code that i have used but i'm unsure if it is in the correct format? Any help would be greatly appreicated ...
written 13 months ago by laural7100
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Comment: C: msmsTests, NA values in test.results output
... BaP_Exp consists of 12 samples, 3 biological replicates of 4 conditions. The data below as been subsetted to two comparisons. BaP_exp is a large MSnSet. Code for analysis mix1=BaP_exp[,BaP_exp$Group %in% c("Ctrl","5")] new=pp.msms.data(mix1) pData(new) ##6 samples H0="y~" H1="y~Group" ...
written 13 months ago by laural7100 • updated 13 months ago by Laurent Gatto1.2k
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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 13 months ago by laural7100

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