User: Beginner

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Beginner50
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Posts by Beginner

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Comment: C: Calculating FPKM from raw counts data using fpkm() in deseq2
... I can actually get the gene lengths from the annotation gtf file. So, if I add that gene_length column to the matrix will it work? ...
written 6 weeks ago by Beginner50
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Calculating FPKM from raw counts data using fpkm() in deseq2
...   I have raw counts data from featureCounts. I actually wanted to do survival analysis. For a specific gene I want to classify the samples into Low and High based on expression cutoff. For that I'm using maxstat package. First I would like to convert raw counts to FPKM. So, I did like following.  ...
geneexpression deseq2 R fpkm() written 6 weeks ago by Beginner50 • updated 6 weeks ago by Michael Love20k
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Comment: C: Voom transformation from counts and normalization to negative values
... Thank you for the explanation !! ...
written 7 weeks ago by Beginner50
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Comment: C: Voom transformation from counts and normalization to negative values
... Thanks a lot for the information. So, basically raw htseq counts with above mentioned voom function in the question gives logCPM values in negative and positive. Is logCPM values are normalized expression data? ...
written 7 weeks ago by Beginner50
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Comment: C: Voom transformation from counts and normalization to negative values
... ok. I see. I'm little confused with this post [https://www.biostars.org/p/153013/#337075] The voom function I mentioned in the my question was taken from this link and applied on raw counts. They say that voom transformation and to normalise data the above mentioned function is used. But not aware w ...
written 7 weeks ago by Beginner50
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Comment: C: Voom transformation from counts and normalization to negative values
... sorry that is not what I want. Anyways here. I see the answer to my question [https://support.bioconductor.org/p/63401/] But not aware about which normalisation method is applied with voom? Is it quantile normalisation? And is it applied across samples? ...
written 7 weeks ago by Beginner50
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Voom transformation from counts and normalization to negative values
... Dear all, I'm using ht-seq raw counts RNA-seq data from TCGA. For Normalizing the data first I used voom() transformation and converted them to log-CPM values. I have used this voom function from Lima package to normalise data. t_index is the samples. The below function I got with some google sear ...
rnaseq limma statistics voom tcga written 7 weeks ago by Beginner50 • updated 7 weeks ago by Ryan C. Thompson7.0k
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Comment: C: DNA methylation analysis without raw data IDAT files
... Hi James, I tried reading the methylation data with readTCGA. But it is not working. May be I'm wrong somewhere The methylation data is in a dataframe "df" with rows as probes and columns like Chromosome, Start position, End position, Gene and Samples like mentioned in my question.  library(minf ...
written 11 weeks ago by Beginner50
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Comment: C: DNA methylation analysis without raw data IDAT files
... yes, I didn't find anything to read methylation data from matrix with champ. Any idea about any other functions? ...
written 11 weeks ago by Beginner50
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DNA methylation analysis without raw data IDAT files
... Hi, I'm interested in working on DNA methylation data. I have downloaded TCGA data from GDC harmonised archive. There are no IDAT files.  IDAT files are available only for GDC legacy archive.  Dataframe "data" is with 485577 probes as rows and 439 columns. There are columns like Chromosome, Start ...
minfi champ R tcga illimina 450k methylation written 12 weeks ago by Beginner50 • updated 12 weeks ago by Yuan Tian40

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