User: tanyabioinfo

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tanyabioinfo20
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Posts by tanyabioinfo

<prev • 25 results • page 1 of 3 • next >
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Deseq2 padjusted values versus pvalue
... I would like to know the difference between p value and p adjusted value which is given an an output by Deseq2 package MY second question is what is the cut off of padj which would be ideal to determine deferentially expressed genes Can anyone please help me with this. Many Thanks Tanya Singh ...
rnaseq deseq2 padjusted written 9 weeks ago by tanyabioinfo20 • updated 9 weeks ago by Michael Love23k
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Deseq2 two controls in design experiment
... Hi I am using Deseq2 for Differential gene expression analysis. I have two controls ( but they are not technical replicates) and one patient. I designed the experiment with two controls together. I was wondering what Deseq2 does when two controls are taken together. Does it takes an average of t ...
rnaseq deseq2 written 11 weeks ago by tanyabioinfo20 • updated 11 weeks ago by Michael Love23k
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(Closed) pheatmap RNA seq data
... Hi    I am plotting a pheatmap using following line in a R code pheatmap(counts_filtered_df,scale="row",cluster_col=FALSE,cluster_row=TRUE,border_color=NA,show_rownames = T)   I want to extract the row names in the same order as shown in pheatmap and the z scores for them.    So basically a n ...
rnaseq R pheatmap written 7 months ago by tanyabioinfo20
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RNAseq tximport Deseq2
...   HI I am using the tximport module to process the output of Salmon. Then I am using the vst(dds) to normalise the data. I understand that the assay for dds is count. How can I process the abundance(TPM) using the vst so that my TPM data is normalised.  My R code looks: txi <- tximport(files, ...
deseq2 tximport written 16 months ago by tanyabioinfo20 • updated 16 months ago by Michael Love23k
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Comment: A: RNA seq tximport
... Hi Michael   Thanks a lot. My TPM data is showing a lot of variation in terms of trends than RPM. Like the tximport output gives a lot of  variation among the replicates. Can you please help me why this would be happening.   Thanks   Tanya ...
written 17 months ago by tanyabioinfo20
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RNA seq tximport
... Hi I am using Salmon to process my RNA seq data. I just want to confirm that the abundance given as an output by the tximport package corresponds to TPM. Many of the cells (the output of tximport) have a value of zero which is making me think about this. Regards Tanya ...
tximport written 17 months ago by tanyabioinfo20
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tximport gene name
... Hi I am doing the following to get the tximport count  matrix with gene name in the first column txdf <- transcripts(EnsDb.Mmusculus.v79, return.type = "DataFrame") txdf$symbol <- mapIds(EnsDb.Mmusculus.v79, txdf$gene_id, "GENENAME", "GENEID") tx2gene <- as.data.frame(txdf[,c("tx_id","sym ...
tximport written 18 months ago by tanyabioinfo20 • updated 18 months ago by Ed Siefker220
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Comment: A: PCA from TPM
... Hi Michael I am now using the follwoing code: txi <- tximport(files, type="salmon", tx2gene=tx2gene, ignoreTxVersion=TRUE,dropInfReps=TRUE) sampleTable <- data.frame(condition =samples$condition,time=factor(samples$time)) rownames(sampleTable) <- colnames(txi$counts) dds <- DESeqDataSe ...
written 18 months ago by tanyabioinfo20
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PCA from TPM
... Hi I am trying to do PCA analysis of my samples. I generated the matrix using the tximport package. I have transcript ids as my rows and the sample names are the columns. txi <- tximport(files, type="salmon", tx2gene=NULL, ignoreTxVersion=TRUE,dropInfReps=TRUE,txOut = TRUE) tpm <- (txi$abun ...
pca tpm tximport written 18 months ago by tanyabioinfo20
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Answer: A: RNA seq tximport
... Thanks James It worked for me.   ...
written 18 months ago by tanyabioinfo20

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Popular Question 8 months ago, created a question with more than 1,000 views. For RNA Seq data analysis using Salmon and tximport

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