User: Vasu

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Vasu270
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Posts by Vasu

<prev • 251 results • page 1 of 26 • next >
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Comment: C: can lnc-RNA target coding RNA?
... I'm actually trying to use `triplexator` to find TTS and TFOs for a specific lncRNA. In the above mentioned papers I see in the second one they used triplexator tool to get TTS and TFOs for MEG3 lncRNA. I'm interested in knowing whether they have given the whole FATSA sequence of MEG3 as input or s ...
written 1 hour ago by Vasu270
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Comment: C: Differential analysis with replicates using edgeR
... Yes, they were the same sample but RNA extraction is done on the next day. As mentioned above Sample1, Sample2 [Controls] and Sample3, Sample4 [Treatment] are done on one day and Sample5, Sample6 [Controls] and Sample7, Sample8 [Treatment] are done on other day All the samples are from the same ce ...
written 6 weeks ago by Vasu270
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Comment: C: Differential analysis with replicates using edgeR
... I had a look into it. This is the first time I'm working with such data. Could you please tell me whether this is right or not. coldata Samples Type Replicates Sample1 Control rep1 Sample2 Control rep1 Sample5 Control rep2 Sample6 Contro ...
written 6 weeks ago by Vasu270
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Comment: C: Differential analysis with replicates using edgeR
... Could you please tell me which section I should check for this. ...
written 6 weeks ago by Vasu270
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Differential analysis with replicates using edgeR
... Hi, I have 8 RNA-Seq samples. Among them 4 are controls and other 4 are treatment. I'm interested in doing differential analysis with edgeR. Following is the column data. Samples Type Sample1 Control Sample2 Control Sample5 Control Sample6 Control Sample7 Treatment Samp ...
differential analysis design matrix rna-seq edger written 6 weeks ago by Vasu270 • updated 27 days ago by Biostar ♦♦ 20
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Comment: C: Sample names for TCGA data from GDC-legacy archive
... Sure, I will be little careful from next time. thanq ...
written 11 weeks ago by Vasu270
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Comment: C: Sample names for TCGA data from GDC-legacy archive
... I just posted the answer how I solved the problem..Yes may be I must have posted the link. I totally forgot about that while posting the solution. Sorry for that. ...
written 11 weeks ago by Vasu270
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Comment: C: Correlation between lncRNA and protein coding genes
... thanks a lot. I got the correlation coefficient values (R). This could tell whether the lncRNA has strong, moderate or weak correlation with other protein coding genes. But I have a small question what is R square in correlation? What does R square tell? ...
written 11 weeks ago by Vasu270
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Comment: C: Correlation between lncRNA and protein coding genes
... Sorry, I'm a bit confused. lets say I have matrix `A` like below. Ensembl ids as rows and Samples as columns. Using raw counts I used `cpm` function and converted them to logCPM values like below. Sample1 Sample2 Sample3 Sample4 Samp ...
written 11 weeks ago by Vasu270
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Comment: C: Correlation between lncRNA and protein coding genes
... so, with this `cor` how to proceed further? I'm interested in doing spearman correlation. ...
written 12 weeks ago by Vasu270

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Popular Question 6 weeks ago, created a question with more than 1,000 views. For Reading Affymetrix data from pd.hugene.2.0.st using oligo for RNA degradation plot
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