User: 1234anjalianjali1234

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Posts by 1234anjalianjali1234

<prev • 46 results • page 1 of 5 • next >
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Comment: C: Design/contrast matrix for Multivariate experimental design in limma
... Thank you for your comment, I am thinking to do meta-analysis instead of combined analysis. ...
written 6 days ago by 1234anjalianjali123430
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Comment: C: Design/contrast matrix for Multivariate experimental design in limma
... Sorry for the inconvenience, how do I delete the post from Bioconductor? ...
written 7 days ago by 1234anjalianjali123430
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Comment: C: Design/contrast matrix for Multivariate experimental design in limma
... Thank you for your suggestions, I will try this Actually, I have applied design model to different chips according to their experimental design, one example I have given below. By looking at my code u will know that I am comfortable doing basic comparisons. But my main problem is to combine all chi ...
written 7 days ago by 1234anjalianjali123430
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Comment: C: Design/contrast matrix for Multivariate experimental design in limma
... I have writte a code for single chip, details are below: Sample Organism Geo protocol_1 Label_1 protocol_2 label_2 ctrl_vs_1h_infested1 Insect GSM200024 T 1hr Cy3 Control 4 hr Cy5 ctrl_vs_1h_infested2 Insect GSM200025 T 1hr Cy3 ...
written 7 days ago by 1234anjalianjali123430
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Comment: C: Design/contrast matrix for Multivariate experimental design in limma
... Thankyou kevin, I have use combat method and yes it modified my data very much, if u can provide me with some better method than combat then I will try it. Also, I have MAlist of each sample. You have included tratment_1 only [what about different time-points]. if u don't mind, would you please t ...
written 7 days ago by 1234anjalianjali123430
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Comment: C: Design/contrast matrix for Multivariate experimental design in limma
... HI kevin, 1.YES, I have used combat to remove the batch effect and want to include batch effect in design/contrast matrix. 2.Actually, I want to find DEG in response to Biotic stress on plants, so yes I want to compare across these organisms with respect to given different time points. ...
written 7 days ago by 1234anjalianjali123430
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Design/contrast matrix for Multivariate experimental design in limma
... Hello, I have four number of Two-color array chips (.gpr files/ genepix) with different time points, infecting organism and with dye swaps and some having biological replicate. it's getting complicated for me to make design/contrast matrix to find differential gene expression. I have done normaliz ...
design matrix limma deg written 7 days ago by 1234anjalianjali123430 • updated 7 days ago by h.mon13k
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Comment: A: motif in set of genes
... HI, What if I don't have "positional frequency matrix". ...
written 11 weeks ago by 1234anjalianjali123430
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Comment: C: SRA file download from NCBI
... thankyou it worked... ...
written 3 months ago by 1234anjalianjali123430
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SRA file download from NCBI
... Hi, I am trying to download SRA file from NCBI-SRA database, But unable to locate download option there, I tried using SRA Toolkit but it failed with an error of not finding that file... can anyone suggest me any other option to download those file... prefetch SRR000001 `Maximum file siz ...
sra file rna-seq written 3 months ago by 1234anjalianjali123430

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