User: ginny

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ginny0
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Posts by ginny

<prev • 11 results • page 1 of 2 • next >
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Comment: C: TCGA miRNA Seq data analysis
... Hi! I'd be really grateful if you could help me out on this issue further because I'm so stuck here.. I have two conditions in my dataset, and I find that for one condition (the "control") ~560 miRNAs have 0 read counts in all the samples, whereas the treatment condition has over 1000s of counts for ...
written 11 weeks ago by ginny0
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Comment: C: Identifying 5p and 3p in miRNA isoform expression data from TCGA for feature sel
... Did you find a way to do this? I want to figure out the 3p/5p forms from the isoform quantification files too, but don't know how or where to begin! ...
written 3 months ago by ginny0
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Comment: C: DESeq2- high number of dysregulated genes in differential gene expression analys
... This is the PCA plot that I've got. I have five sample groups, and I know that four of them are clustering together, but I am still supposed to find DEGs between them! :/ Do you think I have strong batch effects that need to be accounted for? Thanks. ![enter image description here][1] https://ibb ...
written 3 months ago by ginny0
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Comment: C: DESeq2- high number of dysregulated genes in differential gene expression analys
... Thank you so much for responding! I will try using the threshold and see if I get better results. As for the batch effects, I'm not too sure because I have TCGA data, and I can't seem to find the batches that identify each sample. I'm still looking into it, and would want to incorporate it into my d ...
written 3 months ago by ginny0
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Comment: C: DESeq2- high number of dysregulated genes in differential gene expression analys
... Also want to include this- one of my seniors from other lab performed DEG analysis on the same datset using **limma voom**. The number of genes identified from limma voom are fairly lesser, but 70-80% are common from what I obtained from DESeq2, however the fold change differs. Do you think I should ...
written 3 months ago by ginny0
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DESeq2- high number of dysregulated genes in differential gene expression analysis
... Hi. I am a beginner analysing cancer vs normal tissue samples to find the differentially-expressed genes using DESeq2. However, there seems to be one common trend in the results- almost **30-40%** genes are being shown as dysregulated. I keep getting 6000-8000 genes up/downregulated (even 10,000 in ...
R deseq2 rna-seq tcga differentialgeneexpression written 3 months ago by ginny0
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Comment: C: TCGA- which files to download for analyzing differentially expressed miRNAs
... I will try that, thanks! ...
written 4 months ago by ginny0
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Comment: C: DESeq2- How to design data for multiple comparisons?
... Thank you so much!! This is really helpful! ...
written 4 months ago by ginny0
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DESeq2- How to design data for multiple comparisons?
... I am running DESeq2 to find DEGs between multiple samples, but I'm not able to decide what type of design to use, and how to arrange my data? My data the following categories- ---------- **1.DISEASE SUBTYPE | 2. TYPE OF MUTATION** A | mut1 | ...
R deseq2 rna-seq differentialgeneexpression written 4 months ago by ginny0 • updated 4 months ago by rpolicastro3.1k
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Comment: C: TCGA- which files to download for analyzing differentially expressed miRNAs
... Thank you so much! Any idea how can I filter out only the coding genes? ...
written 4 months ago by ginny0

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