User: minio.cz

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minio.cz10
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Posts by minio.cz

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Comment: C: Machine Learning For Cancer Classification - Part 3 - Predicting With A Random F
... Hi, I had the same problem as you. I used processAffyTestData.R script from the first part and it seems that the problem was this part of the script gcrma=gcrma[1:12030,] when I replaced it with gcrma=gcrma[which(!grepl("AFFX", rownames(gcrma))),] the problem disappeared ...
written 4.6 years ago by minio.cz10
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Comment: C: Extracting Publications from sra IDs.
... I cannot be sure, but if I look at individual [samples][1], it lists name of the submitter. Quick googling yielded [this publication][2] that led to GEO dataset GSE65615, which seems to contain at least some of the same patients (although it seems that only thing there not in SRA is type of cancer) ...
written 4.6 years ago by minio.cz10
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Comment: C: GEO Illumina HumanHT-12 V3.0 Series never include Raw Data?
... I looked at some datasets on illumina bead chip and it seems that what you are looking for is the second file (GSE29312_non-normalized.txt.gz).If I am not mistaken, those are intensities measured by scanner (similar to affymetrix CEL files) ...
written 4.6 years ago by minio.cz10
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Comment: C: TCGA clinical data: stage of tumor at time biopsy was taken
... I would try to look directly into pathology reports pdfs, which should contain data based on biopsy. ...
written 4.6 years ago by minio.cz10

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