User: amy16

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amy160
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Posts by amy16

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Comment: C: Code to address batch effect in total number of reads/ sample for DEG using Ball
... Thanks for your advice. -AA ...
written 10 weeks ago by amy160
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Understanding the output from Ballgown for DE
... Hi, I am trying to understand the ballgown output for differential expression analysis. I see only positive values in the fold changes. From the earlier posts, I found that FC<1 indicates down regulation and FC>1 indicates upregulation. In my case, I used 2-group comparisons where the labels ...
ballgown changes written 10 weeks ago by amy160
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Ballgown for more than 2 group comaprison
... Hi, I would like to do three group comparison using Ballgown... When I do, I get the following warning message. I am not sure if it had calculated the differential expression based on the three groups, because this is just a warning message. If not, can you please suggest me on what code I should b ...
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R script to fix the error in dataframe when using ballgown for differentially expression analysis
... Hi, Can someone please correct my code in R for the following error message. I am running Ballgown for differential expression analysis. Error in data.frame(geneNames = ballgown::geneNames(bgfilt_g05), geneIDs = ballgown::geneIDs(bgfilt_g05), :arguments imply differing number of rows: 40738, 173 ...
R ballgown code error written 10 weeks ago by amy160
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Comment: C: Code to address batch effect in total number of reads/ sample for DEG using Ball
... Hi James, Thank you for your suggestion on PCA analysis. I am not a stats person and I am not able understand the Eigen vectors in PCA analysis: Below is the PCA output for the transcript estimate data for one sample; (B1C1 was sequenced in batch 1 and B1C2 , B1C3 were sequenced in the second batch) ...
written 10 weeks ago by amy160
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Comment: C: Code to address batch effect in total number of reads/ sample for DEG using Ball
... Thanks for the reply. Can you please suggest me how I should use the transcript estimate data (output from string tie-merge) for doing PCA plot? -Amy ...
written 11 weeks ago by amy160
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Comment: C: Code to address batch effect in total number of reads/ sample for DEG using Ball
... Hi everyone, Also, to add to my question above, will this difference in number of reads cause a batch effect while estimating the transcripts for each samples. The reason, I am asking this question is that because using stringtie merge function, I merged the transcripts from all samples and then us ...
written 11 weeks ago by amy160
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Code to address batch effect in total number of reads/ sample for DEG using Ballgown
... Hi, I am hoping that someone might be able to give me some advice on adjusting or controlling for batch effects in RNA-Seq data using Ballgown? I have got RNA-seq data for different batches of sequencing for the replicates of the sample. I followed new tuxedo pipeline for my preliminary analysis o ...
batch effects differential expression analysis ballgown r total number of reads written 11 weeks ago by amy160 • updated 11 weeks ago by James W. MacDonald48k
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Comment: C: Including batch effects in the differential expression of gene analysis
... Hi James, Thanks for your reply. I read ballgown vignette and my understanding is that it is possible to include the expected bath effect correction term in the stattest function and adjustvars argument. Please advise me if my I've got my understanding right. Thanks in advance -Amy   ...
written 11 weeks ago by amy160
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Including batch effects in the differential expression of gene analysis
... Hi, I am performing differential expression of gene/transcript analysis using new tuxedo pipeline for the analysis (HISAT2, String tie and Ballgown). Some of the samples within the experiment were sequenced in different batches. Can you please advise me on which step should I include the batch effe ...
ballgown new tuxedo pipleine written 3 months ago by amy160 • updated 3 months ago by James W. MacDonald48k

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