User: ever_wudi

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ever_wudi10
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Posts by ever_wudi

<prev • 12 results • page 1 of 2 • next >
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Comment: C: Generating FPKM matrix accross all samples after stringtie
... I see, thank you very much! ...
written 6 weeks ago by ever_wudi10
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Answer: A: Outputing gexpr() with gene_name (or gene symbol) instead of MSTRG.x gene_id
... I figured out one way to do it. I used whole_tx_table = texpr(my.humandata, 'all') to extract everything into whole_tx_table then do final_fpkm_table = whole_tx_table[c("gene_name","sample 1","sample 2", ..)] to slice out only the gene_name and fpkm values, then write final_fpkm_table to a .cvs ta ...
written 6 weeks ago by ever_wudi10
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Comment: C: Generating FPKM matrix accross all samples after stringtie
... Thanks for the tips. What are the better metrics used now? TPM or some others? ...
written 6 weeks ago by ever_wudi10
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Comment: C: Generating FPKM matrix accross all samples after stringtie
... Hi ATpoint, I have another question. When I use gexpr() to output the matrix, it generates a matrix with MSTRG.x gene ids as identifiers. However, I really need gene_name (or gene symbol) as my gene identifiers for the next step. I tried really hard to fiddle it around and search online but still ca ...
written 6 weeks ago by ever_wudi10
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Outputing gexpr() with gene_name (or gene symbol) instead of MSTRG.x gene_id
... Hi, I am trying to use Ballgown to output gene-sample expression matrix. What I did is `geneexp = gexpr(bg)`, then `write.csv(geneexp, "output.csv", row.names = TRUE)`. However, I could only get it output matrix with MSTRG.x gene ids as identifiers. How can I output the matrix with gene_name (or gen ...
ballgown stringtie rna-seq gene_name written 6 weeks ago by ever_wudi10
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Comment: C: Generating FPKM matrix accross all samples after stringtie
... Thanks for reminding. I didn't intend to feed the count matrix to EdgeR or DESeq2, so I just needed the matrix in the FPKM form. Is there something wrong with the FPKM normalization method? ...
written 6 weeks ago by ever_wudi10
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Comment: C: Generating FPKM matrix accross all samples after stringtie
... I just saw this message, and just realized there is a "tick" sign for marking an accepted answer. I already marked it accepted. ...
written 6 weeks ago by ever_wudi10
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Comment: C: Transformed cancer cell-lines RNA-seq database
... This can be a very useful site and your suggested way makes sense. Thanks a lot, jared.andrews07 (thumb up)! ...
written 7 weeks ago by ever_wudi10
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Transformed cancer cell-lines RNA-seq database
... Hi, I am trying to find a database which has RNA-seq data for cancer cell-lines transformed from normal cells by specific oncogenes or mutated tumor suppressors. I'm not looking for RNA-seq on patient cells (like in TCGA) because they contain many other mutations so the cancer formation is hard to ...
genome rna-seq written 7 weeks ago by ever_wudi10 • updated 7 weeks ago by jared.andrews071.3k
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Comment: C: Generating FPKM matrix accross all samples after stringtie
... Thanks ATpoint, the commands worked. I am very new to R and RNA-seq, did try to search for solutions before but didn't find a satisfactory way. Thanks for the help. ...
written 9 weeks ago by ever_wudi10

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