User: galozs

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galozs20
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Posts by galozs

<prev • 13 results • page 1 of 2 • next >
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Comment: C: Calculate TPM from cuffnorm count data
... What do you mean by "scale the threshold from FPKM=1 to TPM= for each of your samples" ? both correlation matrix I attached were calculated separately on the FPKM / TPM log2 values. Do you mean that the noise threshold in is different for each one of the samples? For example if I used log2(FPKM) = ...
written 2.6 years ago by galozs20
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Comment: C: Calculate TPM from cuffnorm count data
... That what I was thinking though the end values where very strange. (I checked that all the steps were done correctly according to the formula) these are pearson correlations of the log2 FPKM data: ![these are pearson correlations of the log2 FPKM data:][1] and these are the pearson correlations of ...
written 2.6 years ago by galozs20
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Comment: C: Calculate TPM from cuffnorm count data
... Thanks! Do you know if it is OK to do it with the FPKM output values of Cuffnorm? I used the formula that you mentioned and got very wired results when calculated correlation matrix. So I thought that maybe Cuffnorm's FPKM are already manipulated in a way... ...
written 2.6 years ago by galozs20
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Calculate TPM from cuffnorm count data
... Hi, I am working with RNA-seq data and normalizing with Cufflinks' Cuffnorm, whose output is count and FPKM matrices. since I'm comparing gene expression between samples, I wanted to use TPM rather than FPKM. I was wondering about few issues: 1- Can I calculate TPM values directly from the FPKM va ...
fpkm cufflinks tpm cuffnorm rna-seq written 2.6 years ago by galozs20 • updated 2.6 years ago by Macspider3.1k
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Comment: C: gene expression variance equality
... honestly, I used cuffdiff before and realized that using my own code and analysis gives more reliable results. I didn't try the other tools you mentioned, yet. maybe I'll give it a try in the future. ...
written 2.8 years ago by galozs20
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Comment: C: gene expression variance equality
... I am looking at exactly 2 conditions and prefer working with ttest and my own codes. Thanks! ...
written 2.8 years ago by galozs20
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gene expression variance equality
... Hi, I am analyzing RNA seq data and trying to identify differentially expressed genes between to populations using ttest (my data is in triplicates) I was wondering weather I need to check for the variance assumptions before applying ttest. if so- what test will be recommended to use on such data ...
variance test gene expression rna-seq written 2.8 years ago by galozs20 • updated 2.8 years ago by e.rempel890
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Comment: C: re-scale IGV tracks using batch script
... Thanks! I'm looking for a way to extent the options in the batch script and manipulating the scales of the tracks. ...
written 3.4 years ago by galozs20
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re-scale IGV tracks using batch script
... I'm looking for automated way to manage multiple IGV screenshots, though I couldn't find a way to do some very basic (looks like very basic...) manipulation using IGV batch script. 1- Is there a way to change the scale of a specific track (or all of the tracks) ? 2- Is there a way to get the scales ...
rna-seq igv written 3.4 years ago by galozs20
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how does cuffdiff treats replicates with high std?
... Hello, I ran cuffdiff with 3 replicates per condition, trying to find differentially expressed genes. Once I got the results I realized that if one of my replicates is extremely high or extremely low (as if it was just an irregular sample) it diverts the mean of the reps and call it differentially ...
cufflinks cuffdiff rna-seq differential expression written 3.7 years ago by galozs20

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