User: Ahill

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Ahill1.1k
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Posts by Ahill

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Comment: C: There is a way to convert MS data in Bruker ASCII data to MGF?
... Depending on the content of the Bruker file, probably yes. For MSn spectra the MGF format is just a series of fragment ion masses with optional intensities, surrounded by BEGIN IONS and END IONS, as described [here][1]. So if your Bruker ASCII file has fragment ion masses, then you could translate ...
written 6 days ago by Ahill1.1k
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Comment: C: Proteomics - gene covariates for iBAQ measurements.
... iBAQ adjusts for number of observable peptides per protein, so I'm assuming correction for covariates like protein molecular weight or length is not required. Perhaps there are potential biases related to the number of peptides in any protein that are ultimately detectable in a mass spec assay but ...
written 6 weeks ago by Ahill1.1k
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Comment: C: Technology Stack of NCBI (Genbank, GEO, etc.)
... It would be interesting to know more. [This article][1] (2009ish?) has a couple comments from NCBI IEB chief on SRA infrastructure (SQL Server relational meta-db + filesystem storage type design). [1]: http://www.bio-itworld.com/NGS-NCBI.html ...
written 7 weeks ago by Ahill1.1k
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Comment: C: How to choose the threshold of co-expression for gene expression networks
... If you have the input expression dataset that was used to compute MI, you may want to consider doing a randomization test to estimate the type I error rate (false positive rate) as a function of MI threshold. You'd recompute MI in randomly re-assorted input data sets, to determine what the false po ...
written 8 weeks ago by Ahill1.1k
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Comment: C: "Unrecognized token: C" error when using emmax-kin to make kinship matrix for GW
... When generating your .tped, did you use the PLINK --recode12 --output-missing-genotype 0 options? I'm going from the EMMAX web page: [https://genome.sph.umich.edu/wiki/EMMAX#Preparing_Input_Genotype_Files][1] [http://zzz.bwh.harvard.edu/plink/dataman.shtml#recode][2] --recode12 will recode the al ...
written 9 weeks ago by Ahill1.1k
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Comment: C: "Unrecognized token: C" error when using emmax-kin to make kinship matrix for GW
... No experience with emmax-kin, but the source code pasted below suggests it might expect genotypes encoded as 0,1,2, but it encountered the the letter base code 'C' in your TPED. Is that making any sense? == emmax-kin.c lines 430- // if zero_miss_flag is set, assume the genotypes are ...
written 9 weeks ago by Ahill1.1k
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Answer: A: FCS to TXT
... You can use the flowCore package. See [vignette here][1] for example usage. Use the read.FCS() function to read in a FCS file, then write.delim() or write.csv() to write out a .txt or .csv file. [1]: https://www.bioconductor.org/packages/release/bioc/vignettes/flowCore/inst/doc/HowTo-flowCore. ...
written 9 weeks ago by Ahill1.1k
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Comment: C: meta data analysis for clustering
... What's the readout from the screens - is it multiparametric (high content imaging, RNA-Seq, ...) or single parameter (cell survival, reporter assay?). I'm not clear on what signatures you are looking for by clustering - are these clusters of genes that have common readout patterns across RNAi treat ...
written 10 weeks ago by Ahill1.1k
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Answer: A: How do I add ">" symbol to FASTA headers?
... sed 's/^\([^acgt]\)/>\1/' > ...
written 11 weeks ago by Ahill1.1k
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Answer: A: The use of "and" in bioinformatics literature
... The "and" may not guarantee it was normalized first and log2-transformed second... Either approach could have been used, so if the order is important to you I would look more closely at the methods section of the paper for the details of the algorithms used. Example: for Affy oligo arrays, MAS5 m ...
written 3 months ago by Ahill1.1k

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