User: Fatemehsadat Seyednasrollah

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Posts by Fatemehsadat Seyednasrollah

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Comment: C: using easyRNASeq to calculate RPKM values
... Many Thanks. ________________________________________ From: Nicolas Delhomme [delhomme@embl.de] Sent: Tuesday, January 22, 2013 4:46 PM To: Fatemehsadat Seyednasrollah Cc: bioconductor at r-project.org Subject: Re: [BioC] using easyRNASeq to calculate RPKM values Dear Fatemehsadat, It is indeed po ...
written 4.9 years ago by Fatemehsadat Seyednasrollah260
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using easyRNASeq to calculate RPKM values
... Dear list, I have used HTSeq to get the count table of an RNA seq dataset which has 8 biological replicates and two conditions ( so 4 biological replicates for each condition ) and the count table is like below: > head(a) V1 V2 V3 V4 V5 V6 V7 V8 V9 1 1/2-SBSRNA4 3 5 4 4 ...
easyrnaseq written 4.9 years ago by Fatemehsadat Seyednasrollah260 • updated 4.9 years ago by delhomme@embl.de1.2k
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Comment: C: Different number of genes when using HTseq and cuffdiff
... I am using the same gtf file for both. Actually this is why I do not understand this variation between them. I was thinking maybe cuffidff may discard some genes with very low number of counts but I did not find something which support this idea. ________________________________________ From: Steve ...
written 5.0 years ago by Fatemehsadat Seyednasrollah260
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Comment: C: Different number of genes when using HTseq and cuffdiff
... Hi, By more genes I do not mean number of DE genes but the number of total input genes. I have used the same tophat bam files as the input of HTSeq and cuffdiff but in the results regardless of how many DE genes I have, there are different number of total genes. And yes I am using the latest versio ...
written 5.0 years ago by Fatemehsadat Seyednasrollah260
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Different number of genes when using HTseq and cuffdiff
... Hi, I have used the same output tophat bam files both for HTseq (and then DESeq) and cuffdiff to find DE genes. But I do not understand why even when the bam files and references are the same the number of genes are different in the result of cuffdiff and HTseq. Actually I expected to have differ ...
written 5.0 years ago by Fatemehsadat Seyednasrollah260 • updated 5.0 years ago by Steve Lianoglou12k
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Highly Expressed Genes among DE genes in edgeR
... Hi, For an RNA-seq data, I have found the significant DE genes based on FDR < 0.05 using the exactTest() function. Now I need to rank these DE genes based on the expression level (count values). What is the correct way of doing it? Thank you in advance. ...
written 5.0 years ago by Fatemehsadat Seyednasrollah260 • updated 5.0 years ago by Ryan C. Thompson6.2k
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Answer: A: weired bayseq results
... Just I forgot to mention that the order of replicates in the count table has changed in each rerun process. And below is the my code: function (table, each, samplesize) { counttable <- read.delim(table, header = FALSE, row.names = 1) replicates <- c(rep("control", each), rep("treatmen ...
written 5.1 years ago by Fatemehsadat Seyednasrollah260
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weired bayseq results
... Dear list, I have used BaySeq to my RNA-Seq data to extract DE genes and I have several biological replicates for each condition(20 replicates for each condition). The point is that if I rerun the BaySeq over my dataset then the number of detected genes with a specific common FDR will change. Can i ...
bayseq written 5.1 years ago by Fatemehsadat Seyednasrollah260
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Comment: C: BitSeq input data error
... Many Many thanks. With Best Regards, Fatemeh ________________________________________ From: Peter Glaus [glaus@cs.man.ac.uk] Sent: Tuesday, November 06, 2012 5:02 PM To: Fatemehsadat Seyednasrollah Cc: bioconductor at r-project.org Subject: Re: [BioC] BitSeq input data error Dear Fatemeh, as for t ...
written 5.1 years ago by Fatemehsadat Seyednasrollah260
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Comment: C: BitSeq input data error
... Dear Peter, Actually I have a dataset and my final goal is to compare DE genes from BitSeq and cuffdiff. I have used TpHat and as you said the genome reference to map my data and then run cuffdiff. Now do you think it would be a fair comparison of differential expression if I use another type of re ...
written 5.1 years ago by Fatemehsadat Seyednasrollah260

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