User: vinayjrao

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vinayjrao100
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JNCASR, India
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Posts by vinayjrao

<prev • 88 results • page 1 of 9 • next >
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Comment: C: How to extract specific rows based on row number from a file
... Already ditched this method, because I need to select 224 :( ...
written 6 days ago by vinayjrao100
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6 follow
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How to extract specific rows based on row number from a file
... I am working on a RNA-Seq data set consisting of around 24000 rows (genes) and 1100 columns (samples), which is tab separated. For the analysis, I need to choose a specific gene set. It would be very helpful if there is a method to extract rows based on row number? It would be easier that way for me ...
extract shell file-handling written 6 days ago by vinayjrao100 • updated 6 days ago by shenwei3563.6k
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Comment: C: PAM50 subtype classification by genefu
... Dear Matina, I tried transposing the data matrix. It still gave me the same error as the first time. Would it be helpful if I shared the script with you? Thanks. Edit: I was looking into the column names, and there was an error on my part. Transposing the data helped. Thank you very much for all ...
written 12 days ago by vinayjrao100
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Comment: C: PAM50 subtype classification by genefu
... Hi Matina, Thank you for the suggestion, but `do.mapping=T` gave me the following error `Error in data1[, gg.uniq, drop = FALSE] : subscript out of bounds`. Could you also explain how does `do.mapping` affect the run? Thanks. ...
written 14 days ago by vinayjrao100
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PAM50 subtype classification by genefu
... Hello, I'm analyzing TCGA breast cancer data to classify the samples into their respective subtypes, ad then to check if the genes of our study have a subtype specific pattern of expression. To do this, I was suggested to use `genefu`. At the step of classifying the subtypes - `PAM50Base <- mol ...
genefu R bioconductor pam50 rna-seq written 15 days ago by vinayjrao100 • updated 12 days ago by Matina140
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Comment: C: Calculating fpkm from raw counts
... Thank you very much. I'll give it a try, but it certainly helped me understand better. Edit: I considered your suggestion of taking TPM into account, and found that indeed it would be a better method to proceed with my analysis. Thank you. ...
written 19 days ago by vinayjrao100
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Comment: C: Calculating fpkm from raw counts
... Thanks for the reply. I have made an edit in the sample table (corrected a mistake). I have gone through the article, but it just mentions that the difference between rpkm and fpkm is that rpkm is for single-end data, while fpkm is for paired-end data. Also, under what condition is TPM advisable? ...
written 21 days ago by vinayjrao100
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Calculating fpkm from raw counts
... Hello, I have a file consisting of raw counts. For my analysis, I want to normalize the counts by fpkm. The question is, how can I calculate fpkm from raw counts? Also, upon a little reading I found that DESeq2 could do i, but it requires the file to be in DESeq format. Could someone guide me on w ...
R fpkm rna-seq written 22 days ago by vinayjrao100
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Comment: C: RNA-seq analysis between three conditions
... Sure. You could try the hisat2 protocol (new tuxedo protocol), and also other aligners and mergers. [https://www.nature.com/articles/nprot.2016.095][1] [https://www.nature.com/articles/nprot.2013.099#procedure][2] These are two established pipelines, and you could try analyzing the example data t ...
written 7 weeks ago by vinayjrao100
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Comment: C: RNA-seq analysis between three conditions
... Maybe not, but now that you have already invested time in it, you should try the analysis with another pipeline. You would at least know if there was an error in the pipeline, or in the analysis. ...
written 7 weeks ago by vinayjrao100

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Supporter 12 weeks ago, voted at least 25 times.

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