User: Glazko, Galina

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Posts by Glazko, Galina

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Comment: C: PM values for probes in a probeset: background corrected and normalized, but not
... James, I see. Thank you very much! Best regards Galina -----Original Message----- From: James W. MacDonald [mailto:jmacdon@med.umich.edu] Sent: Monday, September 27, 2010 3:56 PM To: Glazko, Galina Cc: bioconductor at stat.math.ethz.ch Subject: Re: [BioC] PM values for probes in a probeset: backgr ...
written 8.6 years ago by Glazko, Galina350
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PM values for probes in a probeset: background corrected and normalized, but not summarized?
... Dear list, I am wondering, is it possible to get Affy PM values for probes in a probeset, which will be background corrected and normalized, but not summarized? I know that I can get just intensities of probes, but do not know whether it is possible to do for them all steps - backgound correction ...
normalization affy written 8.6 years ago by Glazko, Galina350 • updated 8.6 years ago by James W. MacDonald49k
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Comment: C: mouse SNPs
... Steffen, Thank you! This works perfectly fine! Best regards Galina ________________________________ From: Steffen Durinck [mailto:sdurinck@lbl.gov] Sent: Thursday, September 09, 2010 2:28 PM To: Glazko, Galina Cc: Zhu, Julie; bioconductor@stat.math.ethz.ch Subject: Re: [BioC] mouse SNPs annotatio ...
written 8.6 years ago by Glazko, Galina350
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Comment: C: mouse SNPs
... Julie, yes I tried this but it did not work: > getBM(attributes=c("chromosome_name"),filters="ensembl_exon_id",valu es=c("ENSMUSE00000844234"), mart=mart) Error in getBM(attributes = c("chromosome_name"), filters = "ensembl_exon_id", : Invalid filters(s): ensembl_exon_id Please use the functio ...
written 8.6 years ago by Glazko, Galina350
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Answer: A: mouse SNPs
... Dear Vincent and Julie, thank you for the helpful hints! Julie, annotatePeakInBatch works great! But now I have another question: I am trying to annotate these feautures I got back (using Annotation = getAnnotation(mart, featureType="Exon")) and I have this table: space start end width ...
written 8.6 years ago by Glazko, Galina350
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mouse SNPs
... Dear list, I have annotation question and just hope that someone had already similar problem and would be willing to share the experience. I have about 100 mouse SNPs in the format: Chromosome number SNP coordinate (for example:) 16 69067865 I need to annotate ...
snp annotation go hapmap annotate written 8.6 years ago by Glazko, Galina350
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how to find probes' names in probeset
... Dear list, I would appreciate if someone can clarify for me this - seemingly - simple issue: I have probes for the probe set: probes1 <- subset(drosophila2probe, Probe.Set.Name == "1631333_s_at") > as.data.frame(probes1) sequence x y Probe.Set.Name Probe.Interroga ...
probe written 8.7 years ago by Glazko, Galina350 • updated 8.7 years ago by James W. MacDonald49k
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Comment: C: mapping probe sets from yeast2 array to probe sets in hgu133A
... Dear Alexandre, James and list thank you very much for your helpful advises! Alexandre, I am very grateful for these mappings, best Galina ________________________________________ From: Alexandre Kuhn [kuhnam@mail.nih.gov] Sent: Tuesday, August 10, 2010 6:00 PM To: Glazko, Galina; bioconductor at ...
written 8.7 years ago by Glazko, Galina350
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Comment: C: mapping probe sets from yeast2 array to probe sets in hgu133A
... Jim, Thank you for the answer. I would appreciate if you could describe the 'trivial' step: "converting from yeast2 probe IDs to hgu133a probe IDs"? It is not obvious for me, sorry. Best regards Galina -----Original Message----- From: James W. MacDonald [mailto:jmacdon@med.umich.edu] Sent: Frida ...
written 8.7 years ago by Glazko, Galina350
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mapping probe sets from yeast2 array to probe sets in hgu133A
... Dear List, I would appreciate if someone could indicate the easy way how to map probe sets from yeast2 array onto hgu133a probe sets in Bioconductor; May be throughout BioMart? (Mapping should be based on orthologs). I know how to do it in NetAffx, Affymetrix but it takes too much time. Thank you! ...
hgu133a yeast2 probe written 8.7 years ago by Glazko, Galina350 • updated 8.7 years ago by Alexandre Kuhn60

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