User: Manik Garg

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Manik Garg0
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Posts by Manik Garg

<prev • 7 results • page 1 of 1 • next >
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Comment: C: Variance stabilising transformation for machine learning
... Many thanks Michael! I see that the `?varianceStabilizingTransformation` vignette has also been updated with the example. Cheers! > There is some information on how to do this in ?varianceStabilizingTransformation. Although it looks like the example has been removed. ...
written 6 days ago by Manik Garg0
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Comment: C: Variance stabilising transformation for machine learning
... Hi Michael, Do you mean something like this? Please note that for the test data, I will not be having colData for "condition" as this is the category I am trying to predict. Do you suggest creating a dummy column for the same? As `blind = FALSE`, varianceStabilizingTransformation() may consider thi ...
written 7 days ago by Manik Garg0
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Comment: C: Variance stabilising transformation for machine learning
... Many thanks for your speedy reply! I will get back to you if I have any further questions. Cheers! ...
written 7 days ago by Manik Garg0
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Variance stabilising transformation for machine learning
... Hi, I have tried to develop a machine learning model based on a set of differentially expressed genes obtained using DESeq2. Variance stabilising transformation (vst()) was performed for this purpose as it is recommended in the [vignette][1]. But I have applied it to the entire dataset together (as ...
deseq2 rna-seq vst machine-learning written 7 days ago by Manik Garg0 • updated 7 days ago by Michael Love24k
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Comment: C: Is the data after variance stabilising transformation (blind = FALSE) already co
... Thanks for your quick reply! ...
written 9 weeks ago by Manik Garg0
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Is the data after variance stabilising transformation (blind = FALSE) already corrected for covariates?
... Hi, While running DESeq2, I corrected for covariates in the design formula and extracted the vst matrix with blind = FALSE. If I understand it correctly from here (https://www.bioconductor.org/packages/devel/bioc/vignettes/DESeq2/inst/doc/DESeq2.html#blind-dispersion-estimation), blind = FALSE take ...
deseq2 vst covariates written 9 weeks ago by Manik Garg0 • updated 9 weeks ago by Michael Love24k
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Comment: C: WGCNA "bicor" correlation
... I got the same warning even after all my genes passed the goodSamplesGenes() check. Were you able to solve this problem? ...
written 3 months ago by Manik Garg0

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