User: Sara

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Posts by Sara

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Comment: C: Please help with workspace error in R
... Thanks Aaron for your response. Yes, it's not specific to Bioconductor, but it may be a basic question for this forum so I asked here, sorry. I searched a lot before the posting question, however, none of them was helpful, and I'm not sure how accurate is the test using the simulate p-value as one o ...
written 21 days ago by Sara0
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Please help with workspace error in R
... Hi all, I'm running a Fisher exact test with a large amount of data (2 columns and about 3000 rows) on the cluster (Rocks 6.2) with R 3.3.2 , but I got the below workspace error with 1e9 value as workspace: FEXACT error 7. LDSTP is too small for this problem. Try increasing the size of the works ...
R test fisher exact workspace written 22 days ago by Sara0 • updated 21 days ago by Aaron Lun21k
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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 21 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 21 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 21 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 22 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 22 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 22 months ago by Sara0 • updated 22 months ago by Jeff Leek520
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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 2.2 years ago by Sara0 • updated 2.2 years ago by Gordon Smyth35k
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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 2.2 years ago by Sara0 • updated 2.2 years ago by Gordon Smyth35k

Latest awards to Sara

Popular Question 21 months ago, created a question with more than 1,000 views. For The common error with ballgown has not been solved!
Popular Question 21 months 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 21 months ago, created a question with more than 1,000 views. For edgeR normalization method

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