User: Sara

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Posts by Sara

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Please help with ballgown problem
... Hi all, I'm using ballgown package on the stringtie output for differential expression analysis. The .csv file like below: ​       ids   group time rep 1   sample1 control    0   a 2  sample10    drug   24   d 3  sample11    drug   24   d 4   sample2 control    0   a 5   sample3    drug    2   b ...
differential expression ballgown written 9 months ago by Sara0
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Comment: C: The common error with ballgown has not been solved!
... Thank you Alyssa, now another issue appeared that I created a new post.  ...
written 9 months ago by Sara0
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Comment: C: The common error with ballgown has not been solved!
... Thank you, Alyssa for your response!  Actually, I have 2 biological replicates for control (a1 and a2) and three biological replicates for treatment sample that showed with b1-b3, c1-c3, and d1-d3. I have not any technical replicates. I added a "rep" column as bellow, please kindly let me know if i ...
written 9 months ago by Sara0
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Comment: C: The common error with ballgown has not been solved!
... Thank you for your quick response, Alyssa. In response to what you kindly suggested: > data_form$ids [1] sample1 sample10 sample11 sample2 sample3 sample4 sample5 sample6 [9] sample7 sample8 sample9 11 Levels: sample1 sample10 sample11 sample2 sample3 sample4 ... sample9 ​ and > list ...
written 9 months ago by Sara0
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Comment: C: The common error with ballgown has not been solved!
... Thank you Jeff, yes that was the problem. Now another error appeared, while The name and order of sub-folders in the ballgown folder are the same with data_form.csv file and there are 5 files ending to .ctab in each sub-folder. I get error that "Error in ballgown(dataDir = "ballgown", samplePattern ...
written 9 months ago by Sara0
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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 9 months ago by Sara0 • updated 9 months ago by Jeff Leek490
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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 13 months ago by Sara0 • updated 13 months ago by Gordon Smyth32k
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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 13 months ago by Sara0 • updated 13 months ago by Gordon Smyth32k
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Comment: C: Normalization factor in TMM method
... Thanks a lot for your great help. ...
written 13 months 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 13 months ago by Sara0

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