User: peter pfand

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peter pfand80
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Posts by peter pfand

<prev • 49 results • page 1 of 5 • next >
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Comment: C: Exclusion of miRNA microarray probes in PDX models
... 1) I heard that from a colleague and found out the annotation file from Affy (now Thermofisher) contains probesets for many organisms. 2) Nope. I refers in that question to mRNA. Now what I want to know is whether I need to apply the same procedure to miRNAs. ...
written 16 months ago by peter pfand80
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Exclusion of miRNA microarray probes in PDX models
... Hi, I would like to measure expression of miRNAs from (Affy) Clariom D arrays. cDNA comes from a PDX mouse model. Since extracting human genetic material from the PDX implicates extracting some mouse cDNA too, I am not sure whether I should remove the human probes that may hybridise with mouse cDNA ...
clariom pdx affy microarray xenograft written 16 months ago by peter pfand80
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Answer: A: What is the specificity of a Microarray for human vs. mouse when completed for a
... Hi, it might be a bit late answer, but I dealt with such problem a year ago. What I performed was, in summary, the exclusion of human microarray probes that aligned to the mouse transcriptome with `<= 2 mismatches`. I used Clariom D human hg38 arrays from Affymetrix. To flag probes to remove, I ...
written 16 months ago by peter pfand80
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Comment: C: Find out if a protein has an ortholog in EggNog DB
... Hi urema, no, I did not. I sent an email to the first author off the eggNOG paper but he never replied... so I took an alternative approach. ...
written 16 months ago by peter pfand80
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How to automatically find the right species name when there are typos, using Entrez.esearch?
... Hi, First, I'd like to get the lineage of certain species using biopython, but some of the species names (it's the only info I have about species) contain typos. For this reason, when I do: handle = Entrez.esearch(db="Taxonomy", term=species_name, retmode="xml") records = Entrez.read(handl ...
taxonomy biopython entrez written 2.2 years ago by peter pfand80 • updated 2.2 years ago by piet1.7k
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Comment: C: How to choose automatically the most representative (widely used) strain for bac
... Sure, widely used might be misleading. What I mean is the most used strain as a model, such as K12 for E. coli. I need to use all proteomes in general, without focusing on any individual protein. ...
written 2.3 years ago by peter pfand80
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How to choose automatically the most representative (widely used) strain for bacteria species
... Hi, I'd like to build a tree from the uniprot proteomes (see table in [uniprot][1]). However, for many bacterial species, there are plenty of strains I would like to exclude such that I only account for the most widely used or the most representative (in the case of E. coli, K12 strain for instanc ...
choose reference strain bacteria proteomes written 2.3 years ago by peter pfand80
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Best ortholog/inparalog detection between human genes and species from different clades
... Hi, I would like to find the orthologs/inparalogs for a set of human genes wide range of species concerning evolutionary distance: bacteria/archaea, fungi, plants... Initially I've thought of a pairwise method such as Inparanoid, but its code performance is not good enough for a large number of pr ...
ortholog detection evolution written 2.3 years ago by peter pfand80 • updated 2.3 years ago by Rohit1.4k
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Comment: C: How to exclude probes from affy microarray before normalization?
... When I normalize, summarization takes place at gene/probeset level, so at that step I can't remove the probes, just either probesets or genes. ...
written 2.5 years ago by peter pfand80
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Comment: C: How to exclude probes from affy microarray before normalization?
... That's the first thing I tried out, indeed. I read the CEL files and removed the probes from the raw data (HTAFeatureSet) object but I got an error when normalizing. That's why I uninstalled the package (pd.clariom.d.human) and installed a modified (by me) version without the probes. ...
written 2.5 years ago by peter pfand80

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