User: Juliet Hannah

gravatar for Juliet Hannah
Juliet Hannah360
Reputation:
360
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Trusted
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United States
Last seen:
2 months, 2 weeks ago
Joined:
8 years, 4 months ago
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j************@gmail.com

Posts by Juliet Hannah

<prev • 44 results • page 1 of 5 • next >
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concatenating a proteome to use Biostrings pairwiseAlignment
... I have read in a proteome using ``` library("Biostrings") infile <- "proteome.fasta" proteome <- readAAStringSet(infile) ``` I would like to align a list of peptides using Biostrings::pairwiseAlignment so that I can use Biostrings::pid. To do this, it seems I need to convert/concat everyth ...
alignment biostrings written 11 weeks ago by Juliet Hannah360
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Comment: C: Uniprot and UniProt.ws
... Thanks James! "GENECARDS" did indeed link the name. Do you have any suggestions about adding the variant information I describe above? ...
written 11 weeks ago by Juliet Hannah360
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Uniprot and UniProt.ws
... I would like to find the protein sequence for human APOB. I was not able to query by "APOB" so I first looked up the Entrez ID, 338. ``` library(UniProt.ws) human <- UniProt.ws(9606) keys <- c("338") columns <- c("SEQUENCE","UNIPROTKB","PDB") kt <- "ENTREZ_GENE" res <- select(human ...
annotation uniprot identifiers written 11 weeks ago by Juliet Hannah360
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Help with error: 'pd.u133aaofav2 was not found in the BioConductor repository'.
... I am following the gcMap vignette: http://www.bioconductor.org/packages/devel/bioc/vignettes/gCMAPWeb/inst/doc/referenceDatasets.pdf The following data takes a long time to load so I have commented it out: library( ArrayExpress ) library( affy ) # GEOD5258.batch <- ArrayExpress("E-GEOD-5258 ...
pd.u133aaofav2 written 2.6 years ago by Juliet Hannah360 • updated 2.1 years ago by sandmann.t50
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Comment: C: using technical replicates to batch correct
... Thanks for your input. To clarify, I am not trying to use the samples to assess the success of batch correction. I am wondering if I can use the fact that they should be the same to model the batch correction. Thanks again. ...
written 3.0 years ago by Juliet Hannah360
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using technical replicates to batch correct
... Are there tools implemented in Bioconductor that allow one to use technical replicates to batch correct. Meaning, if one has a group of samples that are repeated across known batches, are there tools that can use these samples for batch correction? ...
batch effect written 3.0 years ago by Juliet Hannah360
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affyPLM boxplots for subset of samples
... I have hundreds of arrays for which I would like to obtain NUSE and RLE plots. I would like to make one call to affyPLM, but then plot a subset (boxplot), perhaps a few random samples that cover the entire set. Otherwise, there will be too many samples to show effectively in one boxplot. What is a w ...
affyplm written 3.0 years ago by Juliet Hannah360 • updated 3.0 years ago by James W. MacDonald50k
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Comment: C: limma roast syntax and interpretation
... Thanks, as always, for your help. In this post ( https://support.bioconductor.org/p/60382 ), I had a question about ROAST, and your answer directed me to geneSetTest, which I misinterpreted to mean that one could be substituted for another. I should have read the documentation more carefully. What I ...
written 4.7 years ago by Juliet Hannah360 • updated 4.7 years ago by Gordon Smyth37k
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limma roast syntax and interpretation
... I am using ROAST. I am a little confused by the results, and I wanted to check if my syntax appears correct. I understand that geneSetTest is using a different method than ROAST.  However, I am obtaining substantially different results. Also, I am how does one interpret "Active.Prop=1". Thanks.   ...
limma roast written 4.7 years ago by Juliet Hannah360 • updated 4.7 years ago by Gordon Smyth37k
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Comment: C: limma roast syntax for overall anova
... Hi Gordon, Thanks for your help (and software!). I confusingly showed only the first few rows of the design matrix. I was trying to convey that I left the intercept in. limma gave me the message: > mytt <- topTable(fit,number=Inf) Removing intercept from test coefficients which gives me ...
written 5.0 years ago by Juliet Hannah360 • updated 4.7 years ago by Gordon Smyth37k

Latest awards to Juliet Hannah

Popular Question 2.6 years ago, created a question with more than 1,000 views. For unable to install lumi package
Popular Question 2.6 years ago, created a question with more than 1,000 views. For help with SCAN.UPC and u133aaofav2
Popular Question 2.6 years ago, created a question with more than 1,000 views. For limma roast syntax for overall anova
Popular Question 2.6 years ago, created a question with more than 1,000 views. For limma roast syntax and interpretation
Popular Question 2.6 years ago, created a question with more than 1,000 views. For problems installing xcms package
Popular Question 2.6 years ago, created a question with more than 1,000 views. For limma roast syntax and interpretation

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