User: HKS

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HKS0
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Posts by HKS

<prev • 14 results • page 1 of 2 • next >
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Comment: C: tximport query for un-normalized and TPM data
... yes, I solved it, Thank you.. ...
written 4 weeks ago by HKS0
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Comment: C: tximport query for un-normalized and TPM data
... Is this correct: TPMfromFPKM <- as.numeric(exp(log(txi$abundance) - log(sum(txi$abundance)) + log(1e6))) But this is not giving the output in matrix form, rather the output has long column with values in just one coloumn for all samples.. I want it in matrix form.. ...
written 4 weeks ago by HKS0
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tximport query for un-normalized and TPM data
... I am using .ctab files and type = "stringtie" to calculate txi$abundance, txi$counts, and since the .ctab file contains FPKM values, txi$abundance is giving FPKM matrix. But I want txi$abundance to contain TPM values, and also un-normalised raw counts. I want two types of matrices txi$abundance to ...
tximport written 4 weeks ago by HKS0 • updated 4 weeks ago by Michael Love25k
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Comment: C: tximport not working on tsv files
... No, I also have t_data.ctab files for each sample from StringTie output and I am able to form a matrix out of these files through tximport.. But I want two types : raw counts and TPM values, can tximport give those? I do not want FPKM values.. ...
written 5 weeks ago by HKS0
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Comment: C: tximport not working on tsv files
... Ok, so can I use countsFromAbundance = "ScaledTPM" if I have .ctab files from StringTies Function to generate a matrix of TPM values? and not FPKM values? In the same manner can I use countsFromAbundance = "no" to generate raw counts? Because further I want to use DESeq2 and use raw counts (un-norm ...
written 5 weeks ago by HKS0
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Comment: C: tximport not working on tsv files
... yes, these files are generated in a different way, Is there a way to extract the last column(s) and form a matrix? ...
written 5 weeks ago by HKS0
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Comment: C: tximport not working on tsv files
... In total, I have only 9 columns in my TSV files : Gene ID, Gene Name, Reference, Strand, Start, End, Coverage, FPKM, TPM.. I do not have countsCol and lengthCol in stead I have Coverage .. I want to extract the last two columns in my TSV files i.e. FPKM and TPM .. to form a matrix.. ...
written 5 weeks ago by HKS0
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tximport not working on tsv files
... Hi I am using tximport to make a matrix of all TPM values, I have TSV files for many samples, which looks like: Gene ID Gene Name Reference Strand Start End Coverage FPKM TPM ENSG00000187961.13 KLHL17 chr1 + 960587 965715 4,714223 2,219789 5,030543 ENSG00000187583.10 PLEKHN1 chr1 + 966497 975865 3, ...
tximport written 5 weeks ago by HKS0
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Comment: C: tximport question on the values contained in "counts" and "abundance" matrices
... Yes got it.. the default value for readLength in tximport is 75. Thank you .. ...
written 6 months ago by HKS0
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Comment: C: tximport question on the values contained in "counts" and "abundance" matrices
... yes, i have used the Stringtie argument in tximport: So as you mentioned counts will be calculated by cov * average transcript length / read length so for this gene will it be : 336.726562*4844/? the answer in the output file is : 21748.3891418267 I just want to understand how it is calculated a ...
written 6 months ago by HKS0

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