User: rv

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rv10
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Posts by rv

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Comment: C: HT_HG-U133A_EA probe tab annotation file
... Ok, thank you very much. ...
written 18 months ago by rv10
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Comment: C: HT_HG-U133A_EA probe tab annotation file
... Unfortunately, it seems that the "u133aaofav2cdf" package doesn't contain probe information. I would be interested in doing, with the "u133aaofav2" platform exactly what is done with the "rae230a" platform in this tutorial: https://www.bioconductor.org/packages/3.3/bioc/vignettes/annotate/inst/do ...
written 18 months ago by rv10
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Comment: C: HT_HG-U133A_EA probe tab annotation file
... Thank you @eldronzhou for your answer, I was really searching for a textual, tab delimited, file but, yes, I could access the annotation by R. (I could even serialize the R DataFrame into a tab delimited textual file). Yes, thank you, I didn't consider this option. ...
written 18 months ago by rv10
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HT_HG-U133A_EA probe tab annotation file
... Hello everyone, I am searching for the probe tab annotation file for the Affymetrix platform: ht_hg-u133a_ea wich is used for some drug assays at Connectivity Map database. For the hg-u133a and the ht_hg-u133a platforms, which are also used for the assays, I can find the corresponding probe tab f ...
connectivity map microarray written 18 months ago by rv10 • updated 6 days ago by colinwxl0
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Comment: C: connectivity map vehicle scan id
... Ok, thank you very much @Zhilong Jia. ...
written 21 months ago by rv10
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Comment: C: connectivity map vehicle scan id
... Ok, thank you very much @Zhilong Jia. ...
written 21 months ago by rv10
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connectivity map vehicle scan id
... Hello everyone, I have a problem in understanding the association between perturbation and ctrl array in the cmap instance file When the chip type (array) is HT_HG-U133A, I see associations like these: array perturbation_scan_id vehicle_scan_id HT_HG-U133A ...
connectivity map drug microarray written 21 months ago by rv10 • updated 21 months ago by Zhilong Jia1.1k
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Comment: C: Affymetrix probe id
... Yes, it is. In the tables, the "Probe Interrogation Position" is the position of the 13° (central) base of the probe nucleotide sequence in the gene sequence. I guess that probe ids returned by the "affy" package 1, 2, .. 16 are likely to be sorted by such a position and then they are likely to be ...
written 21 months ago by rv10
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Comment: C: Affymetrix probe id
... Thank you very much @Jason H, I am working with two very similar chips hgu133a and ht-hgu133a in R by the "affy" package. Do you think in this case I could assume the consistency of the probe ids as they are returned by the pm() method from previous example? I know, I should ask the author of the " ...
written 21 months ago by rv10
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Affymetrix probe id
... Hello everyone, I know that affymetrix probeset ids are portable across platforms: the same probeset id 1090_f_at always refers the same gene (probe set). Is it the same for probe ids? Executing, as discussed in the "affy" package vignette, the code: > pm(Dilution, "1090_f_at") on the chi ...
R microarray expression arrays written 21 months ago by rv10

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