User: bioyas

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bioyas0
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Posts by bioyas

<prev • 6 results • page 1 of 1 • next >
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using gene expression matrix for TCseq package to cluster genes
... Hello everyone, I am using the Bioconducter package [TCseq][1] to cluster genes given the gene expression matrix. I have used this package before when I had raw count data and it worked really fine. Now I would like to create the tca object to follow other steps provided in the manual of the pack ...
normalization counts cluster tcseq microwarray written 3 months ago by bioyas0
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Comment: C: removing batch effect using DESeq and sva
... Hi, you are definitely right that's more about sva. I might need to post it with different topic and tags. Thanks ...
written 4 months ago by bioyas0
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Comment: C: removing batch effect using DESeq and sva
... Hi, I have already used 2 SVs as a covariate matrix and passed it to removeBatchEffect() function. After doing so the samples clustering would be disrupted even worse than than before batch correction. I was wondering if this is due to the extra batch effect (still remained in data) or created bia ...
written 4 months ago by bioyas0
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Comment: C: removing batch effect using DESeq and sva
... Thanks for your reply. I look at the link and I am able to apply it to my data. But still I see some batches even after removing batches with the removeBatchEffect from Lima package. I have another question regarding SVA. I tries to define batches manually by looking at SV1 and SV2 (surrogate variab ...
written 5 months ago by bioyas0
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Comment: C: removing batch effect using DESeq and sva
... Thanks for your message. I am looking at F1000 research GateWays to follow the paper. Unfortunately, I was not able to find the FAQ section. Could you please direct me to where I need to the FAQ section so that I can find the answer to my question. I appreciate your help. ...
written 5 months ago by bioyas0
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removing batch effect using DESeq and sva
... Hello, I am working on RNA seq data with 39(13 samples with 3 replicates) samples. I would like to do a PCA analysis. Apparently, there is batch effect in data. I would like to remove these batch effects and see how my samples would cluster after removing batches. I am following the instruction fr ...
sva deseq2 heatmap batch effect pca written 5 months ago by bioyas0 • updated 5 months ago by Michael Love26k

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