User: Beginner

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Beginner50
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Posts by Beginner

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Comment: C: How to create design matrix for differential analysis within the same cell-line
... @Gordon Could you please help me in something about my post. thanq ...
written 10 weeks ago by Beginner50
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How to create design matrix for differential analysis within the same cell-line samples?
... I have a total of 8 samples, 4 controls and 4 Foxcut gene over expressed samples. I have a dataframe `data` with genes as rows and samples as columns with counts. The column data for all the 8 samples look like below with replicate and cell-line information: Samples TYPE ...
rnaseq edger R designmatrix differentialanalysis written 10 weeks ago by Beginner50 • updated 10 weeks ago by Aaron Lun24k
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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 9 months 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 9 months ago by Beginner50 • updated 9 months ago by Michael Love24k
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Comment: C: Voom transformation from counts and normalization to negative values
... Thank you for the explanation !! ...
written 9 months 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 9 months 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 9 months 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 9 months 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 9 months ago by Beginner50 • updated 9 months ago by Ryan C. Thompson7.3k
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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 10 months ago by Beginner50

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