User: Sara

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Sara0
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Posts by Sara

<prev • 39 results • page 2 of 4 • next >
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The common error with ballgown has not been solved!
... Hi all, I have a time course experiment with two conditions, control and treatment, with three biological replicates for each time point except for time 0 (control conditions) that has two biological replicates. I'm using the pipeline of "Hisat, strong tie, ballgown) for data analysis. I have the p ...
software error ballgown written 2.8 years ago by Sara0 • updated 2.8 years ago by Jeff Leek580
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Comment: C: Why the log fold change of some genes returned by edgeR is not compatible with t
... Thank you very much for the comment. Actually, I have done DE analysis with your great help, Gordon, here. I have 5 libraries (unfortunately without replicate) as below: Control-Sensitive cell line (CS) Treatment-Sensitive cell line after 6 hours (TS6) Control-Tolerant cell line (CT) Treatment-T ...
written 3.1 years ago by Sara0 • updated 3.1 years ago by Gordon Smyth39k
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Why the log fold change of some genes returned by edgeR is not compatible with their related FPKM value?
... Hi all experts, I have used Trinity software for doing de novo transcriptome assembly. Then, I used bowtie and RSEM within Trinity package for read mapping and counting. Finally, I got the raw count and FPKM value. I used raw count for doing differential expression analysis by edgeR software, say, ...
edger logfc fpkm written 3.1 years ago by Sara0 • updated 3.1 years ago by Gordon Smyth39k
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Comment: C: Normalization factor in TMM method
... Thanks a lot for your great help. ...
written 3.1 years ago by Sara0
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Comment: C: Normalization factor in TMM method
... Thank you very much, James. It's very helpful, but I'm really sorry for this question, your mean from "samples" in "Dividing the samples by the library size accounts" in paragraph 2 is the mapped read for each gene in a given library? thanks ...
written 3.1 years ago by Sara0
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Normalization factor in TMM method
... Hi all, As many of you do, I apologize for asking a likely dumb question, but I appreciate in advance any clarification from you. As far as I know, calcNormFactors() produces two columns of information. The first is lib.size and the second is norm.factors, which multiplying these two columns togeth ...
normalization edger tmm written 3.1 years ago by Sara0 • updated 3.1 years ago by James W. MacDonald51k
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Comment: C: About differentially expressed genes that found by edgeR
... No response, yet. Please any suggestions! ...
written 3.3 years ago by Sara0
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Comment: C: About differentially expressed genes that found by edgeR
... Thanks for the comment. Regarding the logFC and FPKM, here is the code, this script https://github.com/trinityrnaseq/trinityrnaseq/blob/master/Analysis/DifferentialExpression/run_DE_analysis.pl, within Trinity package made a DE analysis by edgeR (or other software) easy for the beginners, like me. Y ...
written 3.3 years ago by Sara0
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Comment: C: Please share me your helpful comments with edgeR analysis without replicate
... Thanks a lot, Gordon, for following the post. Your help was great. That's right, I'm busy with transcriptome analysis. Yes, there was some interaction as you mentioned, I could get them when the code was corrected by Aaron. Again thank you for all help. ...
written 3.3 years ago by Sara0
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Comment: C: About differentially expressed genes that found by edgeR
... Thank you very much for all responses. They were really helpful. However, I'm still confused about logFC. I did the similar analysis using edgeR within Trinity package, it uses just exact test for DE analysis; here, when two samples,A and B (A-B), compared, genes with higher FPKM in sample B than A ...
written 3.3 years ago by Sara0

Latest awards to Sara

Popular Question 7 months ago, created a question with more than 1,000 views. For edgeR normalization method
Popular Question 12 months ago, created a question with more than 1,000 views. For edgeR normalization method
Popular Question 2.7 years ago, created a question with more than 1,000 views. For The common error with ballgown has not been solved!
Popular Question 2.7 years ago, created a question with more than 1,000 views. For Please help me with the error of " installation of package had non-zero exit status"
Popular Question 2.7 years ago, created a question with more than 1,000 views. For edgeR normalization method

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