User: realnewbie

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realnewbie10
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Posts by realnewbie

<prev • 21 results • page 1 of 3 • next >
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Comment: C: Changes log2FC values of DESeq2
... before baseMean log2FoldChange lfcSE stat pvalue padj ENSDARG00000000001 139.799933351948 0.058625459923395 0.17453323038766 0.335898555210265 0.736947366599281 0.999878824603975 ENSDARG00000000002 532.33641136017 0.065047467376644 0.139490979480544 0.466320242490779 0.640986291495346 0.9998 ...
written 7 months ago by realnewbie10
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Changes log2FC values of DESeq2
... Hi, I've used DESeq2 package to analyze DEGs of my RNA-seq data, (I guess) 4 months ago, and now I wanted to double check the results by re-analyzing the data. Although baseMean values are exactly the same, log2fc, lfcse,stat,pvlaue values have sligtly changed. What could be the reason behind it? ...
#log2fc #changedstatistics #deseq2 written 7 months ago by realnewbie10
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Answer: A: how to fix Kmer count from FastQC?
... Is it because of adapter content? If it is so, there are some tools that might help you in the adapter trimming process. ...
written 8 months ago by realnewbie10
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Comment: C: NextSeq 500 RNA-Seq results
... You are god damn right :) Actually, I am trying very hard. I did not take any course that teaches RNA-seq data analysis from scratch. I am trying to understand and learn every detail in a very short period of time . To combine all the details together and produce something meaningful and right could ...
written 8 months ago by realnewbie10
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Comment: C: Multiple Conditions Testing in DESeq2 with unequal number of replicates
... Yes,you are right. Thanks for your time. However, I was wrong. Sorry for misleading to you. Each treatment is different from each other (but the .1 or.2 meaning relicas for same treatment conditions from different wells),so each control of each treatment is also different(i.e: targeting vector vs em ...
written 8 months ago by realnewbie10
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Comment: C: Multiple Conditions Testing in DESeq2 with unequal number of replicates
... same cell lines with same treatment, but from different wells. ...
written 8 months ago by realnewbie10
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Answer: A: Technical and Biological replicates
... Technical and Biological Replicates clearly explained [here][1]. -Yes,induuude [1]: https://www.youtube.com/watch?v=Exk0OoRG0PQ ...
written 8 months ago by realnewbie10
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Multiple Conditions Testing in DESeq2 with unequal number of replicates
... Hi, I read previous posts about multiple conditions testing. However, my case is a little bit different. I have 3 different groups (plus their controls) with **unequal number of technical replicates**, so I have trouble to how to compare them. First I want to compare each treated sample with its ...
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Comment: C: Tutorials for Library Normalization in DESeq2 and EdgeR
... He is awesome in explaining all of these interesting concepts. ...
written 8 months ago by realnewbie10
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Comment: C: GeneReader RNA-Seq results
... Actually, I haven't used raw sequencing data (fastq files). I used bam files and continue with them through HT-seq. HT-seq gave me the raw counts (for annoatation I used gencode.v19.annotation.gft , the others from ensembl did not work. I dont know why they did not work). ...
written 8 months ago by realnewbie10

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Popular Question 6 months ago, created a question with more than 1,000 views. For TCGA data(RPKM) differential gene expression

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