User: tinmad

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tinmad10
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New User
Location:
Korea, Republic Of
Last seen:
3 years, 2 months ago
Joined:
3 years, 4 months ago
Email:
k************@gmail.com

Posts by tinmad

<prev • 12 results • page 1 of 2 • next >
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Comment: C: DEXSeq for exon counting & package name for human?
... Sorry for the confusion, yes, it was about pasilla package! About your specific comment, do you mean that I have to use DEXSeqDataSetFromHTSeq() function without loading any package? I'm just confused that what should I type instead of 'inDir = system.file("extdata", package="pasilla") from the vign ...
written 3.2 years ago by tinmad10
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Comment: C: DEXSeq for exon counting & package name for human?
... Thank you for your help! For the second question, then is it okay if I follow the same package with the vignette? or Do I have to process any other alternative way? ...
written 3.2 years ago by tinmad10
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DEXSeq for exon counting & package name for human?
... Hi, I want to get exon count so I tried HTSeq-count first (with exon_id option)  but I found that DEXSeq is better for this purpose. I followed the manual (http://bioconductor.org/packages/release/bioc/vignettes/DEXSeq/inst/doc/DEXSeq.pdf) and got a result of reads counting as a *.txt file by runn ...
dexseq exon counting rna-seq written 3.2 years ago by tinmad10 • updated 2.3 years ago by Biostar ♦♦ 20
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Comment: C: How to TMM after HTSeq-count?
... okay... I think I've been mistaken about it..! thank you for the great help! Then if I want to have a matrix with normalized values which is generated using normalization factors from TMM, should I use cpm()? Also, a result from HTSeq-count includes the number of 'no feature', 'ambiguous', 'too lo ...
written 3.2 years ago by tinmad10
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Comment: C: How to TMM after HTSeq-count?
... Thank you for your help. I just checked norm.factors and fouund that it has just one row with 10 values. It's quite confusing as I expected that the result will be a matrix which has the same number of rows and columns with input data (about 30,000 rows and 11 rows, in this case) with normalized v ...
written 3.2 years ago by tinmad10
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Comment: C: How to TMM after HTSeq-count?
... I just want to normalize the counts, not want to find DEGs. Should I do the grouping by DGEList? What should I do if there is no reason to do the grouping? (should I make 10 groups for 10 samples?) Also, I got the result after create DGEList (as a trial) but 1) there is no change in values. Is it ...
written 3.2 years ago by tinmad10
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Comment: C: How to TMM after HTSeq-count?
... before these operations, dim(x) gives [1] 33126   10 and head(x) gives                 sample1    sample2    sample3    ..... A1BG             27           42            53         ..... A1BG.AS1       19           25            21         ..... A1CF              8            21            17        ...
written 3.2 years ago by tinmad10
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Comment: C: How to TMM after HTSeq-count?
... Thank you for your help, I tried it, and got 1 column with 10 rows as a result like below. "x" "1"  1.00593967930787 "2"  0.993971788680494 "3"  0.999906336660367  ... It's quite confusing because I expected that the result will be a matrix which has the same number of rows and columns with input ...
written 3.2 years ago by tinmad10
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Comment: C: How to TMM after HTSeq-count?
... I tried to put 10 HTSeq-count results together, so I made one matrix with them. It has 11 columns; 1st column for gene symbols and other columns are about count values of 11 HTSeq-count results. First error I got before was about that column(x): 'x' must be numeric. ...
written 3.2 years ago by tinmad10
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Comment: C: How to TMM after HTSeq-count?
... Do you mean that I sould use Tophat or something else than BWA? ...
written 3.2 years ago by tinmad10

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